WO2023245117A2 - Compositions et méthodes comprenant des anticorps anti-nrp2 - Google Patents

Compositions et méthodes comprenant des anticorps anti-nrp2 Download PDF

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WO2023245117A2
WO2023245117A2 PCT/US2023/068511 US2023068511W WO2023245117A2 WO 2023245117 A2 WO2023245117 A2 WO 2023245117A2 US 2023068511 W US2023068511 W US 2023068511W WO 2023245117 A2 WO2023245117 A2 WO 2023245117A2
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Prior art keywords
nrp2
antigen
antibody
tissue
binding fragment
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PCT/US2023/068511
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English (en)
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WO2023245117A3 (fr
Inventor
Luke G. BURMAN
Yeeting CHONG
Kaitlyn RAUCH
Leslie A. Nangle
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Atyr Pharma, Inc.
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Publication of WO2023245117A2 publication Critical patent/WO2023245117A2/fr
Publication of WO2023245117A3 publication Critical patent/WO2023245117A3/fr

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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57484—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumor, cancer, neoplasia, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides, metabolites
    • G01N33/57492—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumor, cancer, neoplasia, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides, metabolites involving compounds localized on the membrane of tumor or cancer cells
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
    • C07K2317/33—Crossreactivity, e.g. for species or epitope, or lack of said crossreactivity
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
    • C07K2317/92—Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/52—Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57407—Specifically defined cancers
    • G01N33/57434—Specifically defined cancers of prostate

Definitions

  • the Sequence Listing XML associated with this application is provided in XML file format and is hereby incorporated by reference into the specification.
  • the name of the XML file containing the Sequence Listing XML is ATYR_139_01WO_ST26.xml.
  • the XML file is about 39,352 bytes, was created on June 14, 2023, and is being submitted electronically via USPTO Patent Center.
  • the present disclosure relates to antibodies, and antigen-binding fragments thereof, that specifically bind to select human neuropilin-2 (NRP2) isoforms with low cross-reactivity to human neuropilin-1 (NRP1) and non-human NRP2, and which are optimized for diagnostic uses such as immunohistochemical or immunofluorescence assays. Also included are related compositions and methods for detecting and measuring human NRP2 in a biological sample.
  • Neuropilin-2 is a cell surface receptor that was originally discovered as a neuronal guidance molecule, but has more recently been linked to a broad range of cellular processes, including EMT, cell migration, lymphangiogenesis, and inflammatory conditions. In cancer, NRP2 overexpression is linked to more aggressive growth, cellular invasion, metastatic growth, and resistance development. NRP2 interacts with a broad array of signal transduction, and receptor signaling systems, and is also involved in pinocytosis and efferocytosis. Given the broad range of cellular processes regulated by NRP2, there is a need for high affinity detection antibodies which show high selectivity for human NRP2, bind to all major splice variants of human NRP2, and discriminate between NRP1 and NRP2.
  • the present disclosure satisfies such needs, for example, by describing the development and characterization of a highly-selective, high-affinity antibody that robustly binds to both NRP2a and NRP2b, and which shows low non-specific binding to other cellular components.
  • Embodiments of the present disclosure include an isolated antibody, or an antigen-binding fragment thereof, which binds to a human neuropilin-2 (NRP2) polypeptide, and comprises a heavy chain variable region (VH) sequence that comprises complementary determining region VHCDRI, VHCDR2, and VHCDR3 sequences set forth in SEQ ID NOs: 1-3, respectively; and a light chain variable region (VL) sequence that comprises complementary determining region VLCDRI, VLCDR2, and VLCDR3 sequences, set forth in SEQ ID NOs: 4-6, respectively, including variants thereof having 1, 2, 3, 4, 5, or 6 total alterations across all of the CDR regions.
  • VH heavy chain variable region
  • VHCDRI complementary determining region VHCDRI
  • VHCDR2 VHCDR3 sequences set forth in SEQ ID NOs: 1-3
  • VL light chain variable region
  • the VH sequence comprises an amino acid sequence that is at least 80, 85, 90, 95, 97, 98, 99, or 100% identical to SEQ ID NO: 7
  • the VL sequence comprises an amino acid sequence that is at least 80, 85, 90, 95, 97, 98, 99, or 100% identical to SEQ ID NO: 8.
  • the isolated antibody, or antigen-binding fragment thereof binds to a denatured form of the human NRP2 polypeptide.
  • the isolated antibody, or antigen-binding fragment thereof binds to each of the human NRP2 polypeptides selected from human neuropilin-2a (NRP2a) variant 1 (vl), human NRP2a variant 2 (v2), human NRP2a variant 3 (v3), human neuropilin-2b (NRP2b) variant 4 (v4), and human NRP2b variant 5 (v5), optionally wherein the NRP2 polypeptides are selected from Table Nl.
  • the isolated antibody, or antigenbinding fragment thereof binds to the human NRP2 polypeptide at an epitope that comprises SEQ ID NO: 25.
  • the isolated antibody, or antigen-binding fragment thereof binds to the human NRP2 polypeptide with an affinity of about or less than about 10 nM. In some embodiments, the isolated antibody, or antigen-binding fragment thereof, does not substantially bind to cynomolgus NRP2, mouse NRP2, rat NRP2, or human neuropilin- 1 (NRP1).
  • the isolated antibody, or antigen-binding fragment thereof comprises an IgA (including subclasses IgAl and IgA2), IgD, IgE, IgG (including subclasses IgGl, IgG2, IgG3, and IgG4), or IgM Fc domain.
  • the isolated antibody, or antigen-binding fragment thereof is a monoclonal antibody.
  • the isolated antibody, or antigenbinding fragment thereof comprises a mouse, rabbit, or goat IgG Fc domain, optionally a IgGl or IgG2A Fc domain.
  • the isolated antibody, or antigen-binding fragment thereof is covalently attached to a detectable label.
  • the detectable label is selected from one or more of a fluorophore/fluorescent dye, polymer particle label, metal particle label, iodine- based label, alkaline phosphatase, horseradish peroxidase, luminescent label, radioactive label or radioisotope, nanoparticle, and a quantum dot.
  • a method of determining an amount of a human NRP2 polypeptide in a biological sample comprising
  • identifying the NRP2 -expressing cancer if (i) the amount of NRP2 in the biological sample of cancer tissue from the subject is increased relative to a control or reference, or (ii) the subcellular localization of the NRP2 is increased relative to a control or reference.
  • step (b) comprises determining the ratio of NRP2 localized in the nucleus or nuclear envelope (nuclear NRP2) relative to NRP2 localized on the cell surface (cell surface NRP2), and (c) comprises identifying the NRP2- expressing cancer if the ratio of nuclear NRP2/cell surface NRP2 is increased relative to a control or reference.
  • Some embodiments include administering or causing to be administered to the subject having the NRP2-expressing cancer of (c) at least one NRP2 -targeted therapeutic agent, optionally a therapeutic antibody, or antigen-binding fragment thereof, which binds to human NRP2, and optionally in combination with at least one additional anti -cancer therapy or agent.
  • Some embodiments relate to methods of identifying a subject for NRP2-targeted therapy, comprising
  • step (b) comprises determining the ratio of NRP2 localized in the nucleus or nuclear envelope (nuclear NRP2) relative to NRP2 localized on the cell surface (cell surface NRP2), and (c) comprises identifying the NRP2- expressing cancer if the ratio of nuclear NRP2/cell surface NRP2 is increased relative to a control or reference.
  • Some embodiments include administering or causing to be administered to the subject of (c) at least one NRP2-targeted therapeutic agent, optionally a therapeutic antibody, or antigen-binding fragment thereof, which binds to human NRP2.
  • CRPC castrationresistant prostate cancer
  • AR androgen receptor
  • step (b) comprises determining the ratio of NRP2 localized in the nucleus or nuclear envelope (nuclear NRP2) relative to NRP2 localized on the cell surface (cell surface NRP2), and (c) comprises identifying the subject as being suitable for the aggressive treatment regimen if the ratio of nuclear NRP2/cell surface NRP2 is increased relative to a control or reference.
  • the aggressive treatment regimen comprises at least one NRP2 -targeted therapeutic agent, optionally a therapeutic antibody, or antigen-binding fragment thereof, which binds to human NRP2, in combination with at least one additional anti -cancer therapy or agent optionally at least one chemotherapeutic agent.
  • Some embodiments include methods of identifying NRP2 -mediated drug resistance in a subject, comprising
  • Certain embodiments comprise administering or causing to be administered to the subject of (c) at least one NRP2 -targeted therapeutic agent, optionally a therapeutic antibody, or antigen-binding fragment thereof, which binds to human NRP2, optionally in combination with at least one additional anti-cancer therapy or agent, optionally radiotherapies, cancer immunotherapies, chemotherapeutic agents (optionally DNA damaging agents, DNA repair inhibitors), hormonal therapeutic agents, kinase inhibitors, anti-growth factor therapies, and androgen receptor (AR)-targeted therapies.
  • step (c) comprises correlating a higher increase in subcellular localization of NRP2 to the nucleus or nuclear envelope with a more advanced stage of NRP2-mediated drug resistance.
  • Some embodiments comprise first obtaining the biological sample from a subject, optionally by receiving the biological sample from a healthcare provider, optionally wherein the subject has or is suspected of having a cancer. Certain embodiments comprise providing information to a healthcare provider on the amount or subcellular localization of NRP2 in the biological sample. In certain embodiments, the information on the subcellular localization of NRP2 comprises a ratio of nuclear NRP2/cell surface NRP2 in the biological sample.
  • the biological sample is a biopsy sample.
  • the biopsy sample is a cancer or suspected cancer biopsy sample.
  • the biopsy sample is selected from skin tissue, liver tissue, pancreatic tissue, prostate tissue, mesothelial tissue, epithelial tissue, ovarian tissue, colorectal tissue, gastric tissue, brain tissue, lung tissue, kidney tissue, bladder tissue, uterine tissue, esophageal tissue, cervical tissue, testicular tissue, breast tissue, and mesenchymal tissue such as bone tissue, cartilage tissue, fat tissue, muscle tissue, vascular tissue, blood, or hematopoietic cells/tissue, optionally a liquid biopsy.
  • control or reference is a reference standard, a biological sample from a healthy subject, or a healthy biological sample from the same subject.
  • control is a non-cancerous biological sample from the same subject, optionally of the same tissue type.
  • steps (a) and (b) comprise performing an immunohistochemistry (IHC) or immunofluorescence (IF) assay on the biological sample.
  • the IHC or IF assay comprises a multiplex IHC or IF assay, comprising contacting the biological sample with at least one additional antibody, or antigen-binding fragment thereof, which specifically binds to an additional marker of interest.
  • the additional marker of interest is selected from one or more of signal transduction pathway molecules (VEGF-C, VEGF-A, EGF, IGF, FGF, TGF-beta, VEGFR1, VEGFR2, VEGFR3, CCR7, EGFR1, EGFR2, PDGFR, TGFR1, TGFR2, TGFR3, and c-MET); EMT markers (N-cadherin, E-cadherin, OB-cadherin, ZO-1, a5pi integrin 1, aVp6 integrin, Syndecan-1, FSP1, Cytokeratin, a-SMA, Vimentin 1, P-Catenin, CDH1, EPCAM, claudins, cytokeratins, Snail, Slug, ZEB1, ZEB2, and Twist); lymphangiogenesis markers (lymphatic vessel endothelial hyaluronan receptor-1, or LYVE-1); fibrosis markers (collagen fibers,
  • Figure 1 shows ELISA binding of aNRP2-36v2 to human NRP2v2.
  • Antibody aNRP2-36v2 titrates specifically to the NRP2v2 (SEQ ID NO: 14) protein. All three protein lots tested show similar signals to the NRP2v2 protein indicating similar activity across multiple purification lots.
  • Figure 2 shows aNRP2-36v2 ELISA epitope mapping.
  • Antibody aNRP2-36v2 only binds to the NRP2v2 (SEQ ID NO: 14) and NRP2bv5 (SEQ ID NO: 27) proteins, which indicates the epitope is located in NRP2 residues 642-808.
  • aNRP2-36v2 also does not show any cross-reactivity with mouse, rat, or cynomolgus NRP2.
  • the three different lots also show similar magnitude of signals to each other which also indicates the consistency between the different purification lots.
  • Figures 3A-3B show binding of aNRP2-36v2 to human NRP2v2 and cynomolgus NRP2x2 by BLI.
  • Figure 4 shows aNRP2-36v2 binding to human NRP2 in the presence of blocking peptide.
  • Figure 5 shows Western blotting with aNRP2-36v2.
  • Antibody aNRP2-36v2 only reacts to proteins NRP2v2 (23-855) and NRP2bv5 (23-832) proteins. This data is consistent with the ELISA epitope mapping data. All antibody lots consistently bind the NRP2v2 (23-855) and NRP2bv5 (23- 832) proteins and do not show binding to mouse or rat NRP2, and also do not cross-react with NRP1.
  • Figure 6 shows Western blot of NRP2 with aNRP2-36v2 in the presence of blocking peptide.
  • 1 pg/mL aNRP2-36v2 was incubated with either 5 pg/mL blocking peptide, 5 pg/mL control peptide, or no added peptide, and was then used in Western blotting to detect NRP2. Presence of blocking peptide prevents detection by aNRP2-36v2, indicating that the peptide is binding to the antibody and preventing its association with NRP2.
  • Figure 7 shows IHC detection of NRP2 expression in sarcoidosis skin granulomas by the aNRP2-36v2 antibody.
  • an element means one element or more than one element.
  • amino acid is intended to mean both naturally occurring and non- naturally occurring amino acids as well as amino acid analogs and mimetics.
  • Naturally occurring amino acids include the 20 (L)-amino acids utilized during protein biosynthesis as well as others such as 4-hydroxyproline, hydroxylysine, desmosine, isodesmosine, homocysteine, citrulline and ornithine, for example.
  • Non-naturally occurring amino acids include, for example, (D)-amino acids, norleucine, norvaline, p-fluorophenylalanine, ethionine and the like, which are known to a person skilled in the art.
  • Amino acid analogs include modified forms of naturally and non-naturally occurring amino acids.
  • Such modifications can include, for example, substitution or replacement of chemical groups and moieties on the amino acid or by derivatization of the amino acid.
  • Amino acid mimetics include, for example, organic structures which exhibit functionally similar properties such as charge and charge spacing characteristic of the reference amino acid. For example, an organic structure which mimics Arginine (Arg or R) would have a positive charge moiety located in similar molecular space and having the same degree of mobility as the s-amino group of the side chain of the naturally occurring Arg amino acid.
  • Mimetics also include constrained structures so as to maintain optimal spacing and charge interactions of the amino acid or of the amino acid functional groups. Those skilled in the art know or can determine what structures constitute functionally equivalent amino acid analogs and amino acid mimetics.
  • Biocompatible refers to materials or compounds which are generally not injurious to biological functions of a cell or subject and which will not result in any degree of unacceptable toxicity, including allergenic and disease states.
  • binding refers to a direct association between two molecules, due to, for example, covalent, electrostatic, hydrophobic, and ionic and/or hydrogen-bond interactions, including interactions such as salt bridges and water bridges.
  • biological sample includes a biological material that can be collected from a subject and used in connection with diagnosis or monitoring of biological states.
  • Biological samples can include clinical samples, including body fluid samples, such as body cavity fluids, urinary fluids, cerebrospinal fluids, blood, and other liquid samples of biological origin; and tissue samples, such as biopsy samples, tumor or suspected tumor samples, and other solid samples of biological origin.
  • Biological samples can also include those that are manipulated in some way after their collection, such as by treatment with reagents, culturing, solubilization, enrichment for certain biological constituents, cultures or cells derived therefrom, and the progeny thereof.
  • coding sequence is meant any nucleic acid sequence that contributes to the code for the polypeptide product of a gene.
  • non-coding sequence refers to any nucleic acid sequence that does not directly contribute to the code for the polypeptide product of a gene.
  • conjugate includes an entity formed as a result of covalent or non-covalent attachment or linkage of an agent or other molecule, e.g., a detectable label, to an antibody described herein.
  • a “control” such as a “control subject” or “control tissue” includes a healthy subject or a healthy tissue sample, for example, which is not pathological or diseased.
  • a control includes a non-diseased (e.g., non-cancerous) tissue from a different, healthy subject or the same subject being tested or diagnosed.
  • a control can also include a reference standard, for example, a standard value generated from one or more healthy subjects or tissues (e.g., a population or cohort of healthy subjects or tissues).
  • the terms “function” and “functional” and the like refer to a biological, enzymatic, or therapeutic function.
  • Homology refers to the percentage number of amino acids that are identical or constitute conservative substitutions. Homology may be determined using sequence comparison programs such as GAP (Deveraux et al., Nucleic Acids Research. 12, 387-395, 1984), which is incorporated herein by reference. In this way sequences of a similar or substantially different length to those cited herein could be compared by insertion of gaps into the alignment, such gaps being determined, for example, by the comparison algorithm used by GAP.
  • isolated is meant material that is substantially or essentially free from components that normally accompany it in its native state.
  • an “isolated peptide” or an “isolated polypeptide” and the like, as used herein, includes the in vitro isolation and/or purification of a peptide or polypeptide molecule from its natural cellular environment, and from association with other components of the cell; i.e., it is not significantly associated with in vivo substances.
  • the isolated polypeptide is an antibody.
  • modulating and “altering” include “increasing,” “enhancing” or “stimulating,” as well as “decreasing” or “reducing,” typically in a statistically significant or a physiologically significant amount or degree relative to a control.
  • An “increased,” “stimulated” or “enhanced” amount is typically a “statistically significant” amount, and may include an increase that is 1.1, 1.2, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100 or more times (e.g., 500, 1000 times) (including all integers and ranges in between e.g., 1.5, 1.6, 1.7.
  • a “decreased” or “reduced” amount is typically a “statistically significant” amount, and may include a 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18% , 19%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% decrease (including all integers and ranges in between) in the amount produced by no composition (e.g., the absence of an agent) or a control composition. Examples of comparisons and “statistically significant” amounts are described herein.
  • the “purity” of any given agent (e.g., an antibody) in a composition may be specifically defined.
  • certain compositions may comprise an agent that is at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% pure, including all decimals in between, as measured, for example and by no means limiting, by high-performance liquid chromatography (HPLC), a well-known form of column chromatography used frequently in biochemistry and analytical chemistry to separate, identify, and quantify compounds.
  • HPLC high-performance liquid chromatography
  • polypeptide and protein are used interchangeably herein to refer to a polymer of amino acid residues and to variants and synthetic analogues of the same. Thus, these terms apply to amino acid polymers in which one or more amino acid residues are synthetic non-naturally occurring amino acids, such as a chemical analogue of a corresponding naturally occurring amino acid, as well as to naturally-occurring amino acid polymers.
  • the polypeptides described herein are not limited to a specific length of the product; thus, peptides, oligopeptides, and proteins are included within the definition of polypeptide, and such terms may be used interchangeably herein unless specifically indicated otherwise.
  • polypeptides described herein may also comprise post-expression modifications, such as glycosylations, acetylations, phosphorylations, and the like, as well as other modifications known in the art, both naturally occurring and non-naturally occurring.
  • a polypeptide may be an entire protein, or a subsequence, fragment, variant, or derivative thereof.
  • polynucleotide and “nucleic acid” includes mRNA, RNA, cRNA, cDNA, and DNA.
  • the term typically refers to polymeric form of nucleotides of at least 10 bases in length, either ribonucleotides or deoxynucleotides or a modified form of either type of nucleotide.
  • the term includes single and double stranded forms of DNA.
  • isolated DNA and “isolated polynucleotide” and “isolated nucleic acid” refer to a molecule that has been isolated free of total genomic DNA of a particular species.
  • an isolated DNA segment encoding a polypeptide refers to a DNA segment that contains one or more coding sequences yet is substantially isolated away from, or purified free from, total genomic DNA of the species from which the DNA segment is obtained. Also included are non-coding polynucleotides (e.g., primers, probes, oligonucleotides), which do not encode a polypeptide. Also included are recombinant vectors, including, for example, expression vectors, viral vectors, plasmids, cosmids, phagemids, phage, viruses, and the like.
  • Additional coding or non-coding sequences may, but need not, be present within a polynucleotide described herein, and a polynucleotide may, but need not, be linked to other molecules and/or support materials.
  • a polynucleotide or expressible polynucleotides regardless of the length of the coding sequence itself, may be combined with other sequences, for example, expression control sequences.
  • “Expression control sequences” include regulatory sequences of nucleic acids, or the corresponding amino acids, such as promoters, leaders, enhancers, introns, recognition motifs for RNA, or DNA binding proteins, polyadenylation signals, terminators, internal ribosome entry sites (IRES), secretion signals, subcellular localization signals, and the like, which have the ability to affect the transcription or translation, or subcellular, or cellular location of a coding sequence in a host cell. Exemplary expression control sequences are described in Goeddel; Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990).
  • a “promoter” is a DNA regulatory region capable of binding RNA polymerase in a cell and initiating transcription of a downstream (3’ direction) coding sequence.
  • the promoter sequence is bounded at its 3 ’ terminus by the transcription initiation site and extends upstream (5 ’ direction) to include the minimum number of bases or elements necessary to initiate transcription at levels detectable above background.
  • a transcription initiation site (conveniently defined by mapping with nuclease SI) can be found within a promoter sequence, as well as protein binding domains (consensus sequences) responsible for the binding of RNA polymerase.
  • Eukaryotic promoters can often, but not always, contain “TATA” boxes and “CAT” boxes.
  • Prokaryotic promoters contain Shine- Dalgamo sequences in addition to the -10 and -35 consensus sequences.
  • reference sequence refers generally to a nucleic acid coding sequence, or amino acid sequence, to which another sequence is being compared. All polypeptide and polynucleotide sequences described herein are included as references sequences, including those described by name and those described in the Tables and the Sequence Listing.
  • sequence identity or, for example, comprising a “sequence 50% identical to,” as used herein, refer to the extent that sequences are identical on a nucleotide-by-nucleotide basis or an amino acid-by-amino acid basis over a window of comparison.
  • a “percentage of sequence identity” may be calculated by comparing two optimally aligned sequences over the window of comparison, determining the number of positions at which the identical nucleic acid base (e.g., A, T, C, G, I) or the identical amino acid residue (e.g., Ala, Pro, Ser, Thr, Gly, Vai, Leu, He, Phe, Tyr, Trp, Lys, Arg, His, Asp, Glu, Asn, Gin, Cys and Met) occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison (i.e., the window size), and multiplying the result by 100 to yield the percentage of sequence identity.
  • the identical nucleic acid base e.g., A, T, C, G, I
  • the identical amino acid residue e.g., Ala, Pro, Ser, Thr, Gly, Vai, Leu, He, Phe, Tyr, Trp, Lys,
  • nucleotides and polypeptides having at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% sequence identity to any of the reference sequences described herein (see, e.g., Sequence Listing), typically wherein the polypeptide variant maintains at least one biological activity of the reference polypeptide.
  • references to describe sequence relationships between two or more polynucleotides or polypeptides include “reference sequence,” “comparison window,” “sequence identity,” “percentage of sequence identity,” and “substantial identity.”
  • a “reference sequence” is at least 12 but frequently 15 to 18 and often at least 25 monomer units, inclusive of nucleotides and amino acid residues, in length.
  • two polynucleotides may each comprise (1) a sequence (i.e., only a portion of the complete polynucleotide sequence) that is similar between the two polynucleotides, and (2) a sequence that is divergent between the two polynucleotides
  • sequence comparisons between two (or more) polynucleotides are typically performed by comparing sequences of the two polynucleotides over a “comparison window” to identify and compare local regions of sequence similarity.
  • a “comparison window” refers to a conceptual segment of at least 6 contiguous positions, usually about 50 to about 100, more usually about 100 to about 150 in which a sequence is compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned.
  • the comparison window may comprise additions or deletions (i.e., gaps) of about 20% or less as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences.
  • Optimal alignment of sequences for aligning a comparison window may be conducted by computerized implementations of algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package Release 7.0, Genetics Computer Group, 575 Science Drive Madison, WI, USA) or by inspection and the best alignment (i.e., resulting in the highest percentage homology over the comparison window) generated by any of the various methods selected.
  • GAP Garnier et al.
  • FASTA Altschul et al.
  • TFASTA Pearson-binding Alignment of sequences for aligning a comparison window
  • Statistical significance By “statistically significant,” it is meant that the result was unlikely to have occurred by chance. Statistical significance can be determined by any method known in the art. Commonly used measures of significance include the p-value, which is the frequency or probability with which the observed event would occur, if the null hypothesis were true. If the obtained p-value is smaller than the significance level, then the null hypothesis is rejected. In simple cases, the significance level is defined at a p-value of 0.05 or less.
  • the term “solubility” refers to the property of an antibody described herein to dissolve in a liquid solvent and form a homogeneous solution.
  • Solubility is typically expressed as a concentration, either by mass of solute per unit volume of solvent (g of solute per kg of solvent, g per dL (100 mL), mg/mL, etc.), molarity, molality, mole fraction or other similar descriptions of concentration.
  • the maximum equilibrium amount of solute that can dissolve per amount of solvent is the solubility of that solute in that solvent under the specified conditions, including temperature, pressure, pH, and the nature of the solvent.
  • solubility is measured at physiological pH, or other pH, for example, at pH 5.0, pH 6.0, pH 7.0, or pH 7.4.
  • solubility is measured in water or a physiological buffer such as PBS or NaCl (with or without NaP).
  • solubility is measured at relatively lower pH (e.g., pH 6.0) and relatively higher salt (e.g., 500 mM NaCl and 10 mM NaPCL).
  • solubility is measured in a biological fluid (solvent) such as blood or serum.
  • the temperature can be about room temperature (e.g., about 20, 21, 22, 23, 24, 25 °C) or about body temperature ( ⁇ 37 °C).
  • an antibody has a solubility of at least about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, or 30 mg/mL at room temperature or at about 37 °C.
  • a “subject,” as used herein, includes any animal that exhibits a symptom or condition, or is at risk for or suspected of exhibiting a symptom or condition, which can be diagnosed with an antibody described herein.
  • Suitable subjects include laboratory animals (such as mouse, rat, rabbit, or guinea pig), farm animals, and domestic animals or pets (such as a cat or dog).
  • Non-human primates and, preferably, human patients, are included.
  • a “subject subpopulation” or “patient subpopulation,” as used herein, includes a subject or patient subset characterized as having one or more distinctive measurable and/or identifiable characteristics that distinguishes the subject or patient subset from others in the broader disease category (e.g., cancer) to which it belongs. Such characteristics include disease subcategories, gender, lifestyle, health history, organs/tissues involved, treatment history, etc.
  • a patient or subject subpopulation is characterized by the (e.g., increased) amount or levels of a NRP2 polypeptide in a biological sample, for example, a tumor sample.
  • a subject “at risk” of developing a disease, or adverse reaction may or may not have detectable disease, or symptoms of disease, and may or may not have displayed detectable disease or symptoms of disease prior to the treatment methods described herein.
  • “At risk” denotes that a subject has one or more risk factors, which are measurable parameters that correlate with development of a disease, as described herein and known in the art. A subject having one or more of these risk factors has a higher probability of developing disease, or an adverse reaction than a subject without one or more of these risk factor(s).
  • compositions may be “substantially free” of cell proteins, membranes, nucleic acids, endotoxins, or other contaminants.
  • “Therapeutic response” refers to improvement of symptoms (whether or not sustained) based on administration of one or more therapeutic agents.
  • terapéuticaally effective amount is the amount of an agent (e.g., anti-NRP2 antibody) needed to elicit the desired biological response following administration.
  • an agent e.g., anti-NRP2 antibody
  • treatment of a subject (e.g., a mammal, such as a human) or a cell is any type of intervention used in an attempt to alter the natural course of the individual or cell.
  • Treatment includes, but is not limited to, administration of a pharmaceutical composition, and may be performed either prophylactically or subsequent to the initiation of a pathologic event or contact with an etiologic agent.
  • prophylactic treatments which can be directed to reducing the rate of progression of the disease or condition being treated, delaying the onset of that disease or condition, or reducing the severity of its onset.
  • “Treatment” or “prophylaxis” does not necessarily indicate complete eradication, cure, or prevention of the disease or condition, or associated symptoms thereof.
  • wild-type refers to a gene or gene product (e.g., a polypeptide) that is most frequently observed in a population and is thus arbitrarily designed the “normal” or “wild-type” form of the gene.
  • Embodiments of the present disclosure relate to antibodies, and an antigen-binding fragments thereof, which bind to a human neuropilin-2 (NRP2) polypeptide.
  • NRP2 is a single transmembrane receptor with a predominant extracellular region containing two CUB domains (al/a2 combined domain), two Factor V/VIII homology domains (bl/b2 combined domain), a MAM domain (c domain), and a short juxtamembrane region that connects the c domain to the transmembrane domain (which traverses the plasma membrane).
  • NRP2 is typically expressed in vivo as a mixture of various closely related splice variants, which are often grouped together as NRP2a, which comprises “isoforms” or “variants” vl, v2, and v3, and NRP2b, which comprises isoforms or variants v4 and v5.
  • Variant v6 is a soluble form of NRP2 which is found in circulation.
  • the NRP2a and NRP2b splice variants have identical amino acid sequences over the al, a2, bl, b2 and c domain, but differ in sequence over the juxtamembrane, transmembrane, and cytoplasmic regions.
  • the NRP2a variants vl, v2, and v3 also differ in amino acid sequence over these regions based on their pattern of alternative splicing, with NRP2a vl (93 laa) and NRP2a v2 (926aa) having larger inserts compared to the relatively smaller NRP2a v3 (909aa).
  • NRP2a The different sizes of these alternatively spliced forms of NRP2a reflect a loss of a 5 amino acid stretch at the N-terminus of the juxtamembrane sequence from vl to v2, then a further loss of 17 amino acids immediately C-terminal to the 5 amino acid deletion in the v3 variant.
  • the C-terminal half of the juxtamembrane region, transmembrane helix, and cytoplasmic domain remains identical in all three NRP2a variants.
  • NRP2a and NRP2b the ala2 combined domain of NRP2 interacts with sema region of the semaphorins, and the bl domain interacts with the semaphorin PSI and Ig-like domains.
  • NRP2 has a higher affinity for SEMA3F and 3G; in contrast, SEMAs 3A, 3B and 3E preferentially interact with NRP1.
  • Both NRP1 and NRP2 have similar affinity for SEMA 3C.
  • the blb2 combined domain of NRP2 interacts with several growth factors containing heparin-binding domains, including VEGF C & D, placental growth factor (PlGF)-2, fibroblast growth factor (FGF), galectin, hepatocyte growth factor (HGF), platelet derived growth factor (PDGF), and transforming growth factor (TGF)-beta (see, for example, Prud’Neill et al., Oncotarget. 3:921-939, 2012).
  • VEGF C & D placental growth factor
  • FGF fibroblast growth factor
  • HGF hepatocyte growth factor
  • PDGF platelet derived growth factor
  • TGF transforming growth factor
  • integrins and growth factor receptors like VEGFR2 and VEGFR3, TGF-beta receptors, c-Met, EGFR, FGFR, PDGFR, have been shown to interact with NRPs and in general appear to increase the affinity of each ligand for its receptor and to modulate downstream signaling.
  • the c domain (Mam) domain does not appear to be directly required for ligand binding, but may impact ligand specificity, receptor signaling, and NRP2 dimerization.
  • Neuropilin-2 modulates a broad range of cellular functions through its roles as an essential cell surface receptor and co-receptor for a variety of ligands (see, e.g., Guo and Vander Kooi, J. Cell. Biol. 290 No 49: 29120-29126, 2015). Additionally, NRP2 is a key player in the pathophysiology of many diseases (e.g., “NRP2-associated diseases”, as described herein) and interacts with a broad array of soluble ligands including semaphorin 3F, VEGF-C and D, and TGF-beta, and an array of cellular receptors and co-factors.
  • NRP2 is a key player in the pathophysiology of many diseases (e.g., “NRP2-associated diseases”, as described herein) and interacts with a broad array of soluble ligands including semaphorin 3F, VEGF-C and D, and TGF-beta, and an array of cellular receptors and
  • NRP2 directly contributes to cancer stem cell maintenance, and survival leading to increased tumor initiation, survival, chemo- and radio-resistance development, and metastasis (see, e.g., and Samuel et al., PLoS ONE 6(10) e23208, 2011), Prud’Neill et al., Oncotarget 3:921-939, 2012).
  • NRP2b isoforms are specifically implicated in supporting TGFp-mediated progression in lung cancer (Gemmill et al., Sci Signal.
  • an antibody, or an antigen-binding fragment thereof is characterized by or comprises a heavy chain variable region (VH) sequence that comprises complementary determining region VHCDRI, VHCDR2, and VHCDR3 sequences, and a light chain variable region (VL) sequence that comprises complementary determining region VLCDRI, VLCDR2, and VLCDR3 sequences.
  • VH heavy chain variable region
  • VL light chain variable region
  • Exemplary V H , V H CDR1, V H CDR2, V H CDR3, V L , VLCDRI, V L CDR2, and V L CDR3 sequences are provided in Table SI and Table S2 below.
  • an antibody or antigen-binding fragment thereof comprises: a heavy chain variable region (VH) sequence that comprises complementary determining region VHCDRI, VHCDR2, and VHCDR3 sequences selected from Table SI and variants thereof which specifically bind to a human NRP2 polypeptide or an epitope thereof (selected, for example, from Table Nl); and a light chain variable region (VL) sequence that comprises complementary determining region VLCDRI, VLCDR2, and VLCDR3 sequences selected from Table SI and variants thereof which specifically bind to the human NRP2 polypeptide or an epitope thereof (selected, for example, from Table Nl).
  • VH heavy chain variable region
  • VHCDR2 VHCDR2
  • VHCDR3 selected from Table SI and variants thereof which specifically bind to a human NRP2 polypeptide or an epitope thereof
  • the VHCDRI, VHCDR2, and VHCDR3 sequences comprise SEQ ID NOs: 1-3, respectively, and the VLCDRI, VLCDR2, and VLCDR3 sequences comprise SEQ ID NOs: 4-6, respectively.
  • variants thereof including affinity matured variants, which bind to a human NRP2 polypeptide or epitope thereof (see, for example, Table Nl), for example, variants having 1, 2, 3, 4, 5, or 6 total alterations across all of the CDR regions, for example, one or more the VHCDRI, V H CDR2, V H CDR3, VLCDRI, V L CDR2, and/or V L CDR3 sequences described herein.
  • Exemplary “alterations” include amino acid substitutions, additions, and deletions.
  • the VH sequence comprises a sequence that is at least 80, 85, 90, 95, 97, 98, 99, or 100% identical to a sequence selected from Table S2, including, for example, wherein the VH sequence has 1, 2, 3, 4, 5, or 6 total alterations in one or more framework regions.
  • the VL sequence comprises a sequence that is at least 80, 85, 90, 95, 97, 98, 99, or 100% identical to a sequence selected from Table S2, including, for example, wherein the VL sequence has 1, 2, 3, 4, 5, or 6 total alterations in one or more framework regions.
  • the VH sequence is at least 80, 85, 90, 95, 97, 98, 99, or 100% identical to SEQ ID NO: 7
  • the VL sequence is at least 80, 85, 90, 95, 97, 98, 99, or 100% identical to SEQ ID NO: 8.
  • Certain variants have 1, 2, 3, 4, 5, or 6 total alterations in one or more framework regions, which bind to a human NRP2 polypeptide or epitope thereof (see, for example, Table Nl).
  • exemplary “alterations” include amino acid substitutions, additions, and deletions.
  • antibody encompasses not only intact polyclonal or monoclonal antibodies, but also fragments thereof (such as dAb, Fab, Fab’, F(ab’)2, Fv), single chain (scFv), synthetic variants thereof, naturally occurring variants, fusion proteins comprising an antibody portion with an antigen-binding fragment of the required specificity, humanized antibodies, chimeric antibodies, and any other modified configuration of the immunoglobulin molecule that comprises an antigen-binding site or fragment (epitope recognition site) of the required specificity. Certain features and characteristics of antibodies (and antigen-binding fragments thereof) are described in greater detail herein.
  • an antibody or antigen-binding fragment can be of essentially any type.
  • an antibody is an immunoglobulin molecule capable of specific binding to a target, such as an immune checkpoint molecule, through at least one epitope recognition site, located in the variable region of the immunoglobulin molecule.
  • an antigen-binding fragment refers to a polypeptide fragment that contains at least one CDR of an immunoglobulin heavy and/or light chain that binds to the antigen of interest.
  • an antigen-binding fragment of the herein described antibodies may comprise 1, 2, 3, 4, 5, or all 6 CDRs of a VH and VL sequence from antibodies that bind to a target molecule.
  • an antibody or antigen-binding fragment thereof specifically binds to a target molecule, for example, an NRP2 polypeptide or an epitope or complex thereof, with an equilibrium dissociation constant that is about or ranges from about ⁇ 10 -7 M to about 10’ 8 M.
  • the equilibrium dissociation constant is about or ranges from about ⁇ 10 -9 M to about ⁇ 1O 10 M.
  • an antibody or antigen-binding fragment thereof has an affinity (Kd or EC50) for a target molecule (to which it specifically binds) of about, at least about, or less than about, 0.01, 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, or 50 nM.
  • a molecule such as a polypeptide or antibody is said to exhibit “specific binding” or “preferential binding” if it reacts or associates more frequently, more rapidly, with greater duration and/or with greater affinity with a particular cell, substance, or particular epitope than it does with alternative cells or substances, or epitopes.
  • An antibody “specifically binds” or “preferentially binds” to a target molecule or epitope if it binds with greater affinity, avidity, more readily, and/or with greater duration than it binds to other substances or epitopes, for example, by a statistically significant amount.
  • one member of the pair of molecules that exhibit specific binding has an area on its surface, or a cavity, which specifically binds to and is therefore complementary to a particular spatial and/or polar organization of the other member of the pair of molecules.
  • the members of the pair have the property of binding specifically to each other.
  • an antibody that specifically or preferentially binds to a specific epitope is an antibody that binds that specific epitope with greater affinity, avidity, more readily, and/or with greater duration than it binds to other epitopes. It is also understood by reading this definition that, for example, an antibody (or moiety or epitope) that specifically or preferentially binds to a first target may or may not specifically or preferentially bind to a second target.
  • an antibody is specific for a particular epitope which is carried by a number of antigens, in which case the specific binding member carrying the antigen-binding fragment or domain will be able to bind to the various antigens carrying the epitope; for example, it may be cross reactive to a number of different forms of a target antigen from multiple species that share a common epitope.
  • Immunological binding generally refers to the non-covalent interactions of the type which occur between an immunoglobulin molecule and an antigen for which the immunoglobulin is specific, for example by way of illustration and not limitation, as a result of electrostatic, ionic, hydrophilic and/or hydrophobic attractions or repulsion, steric forces, hydrogen bonding, van der Waals forces, and other interactions.
  • the strength, or affinity of immunological binding interactions can be expressed in terms of the dissociation constant (Kd) of the interaction, wherein a smaller Kd represents a greater affinity.
  • Immunological binding properties of selected polypeptides can be quantified using methods well known in the art.
  • One such method entails measuring the rates of antigen-binding site/antigen complex formation and dissociation, wherein those rates depend on the concentrations of the complex partners, the affinity of the interaction, and on geometric parameters that equally influence the rate in both directions.
  • both the “on rate constant” (Kon) and the “off rate constant” (Koff) can be determined by calculation of the concentrations and the actual rates of association and dissociation.
  • the ratio of Koff /Kon enables cancellation of all parameters not related to affinity, and is thus equal to the dissociation constant Kd.
  • affinity includes the equilibrium constant for the reversible binding of two agents and is expressed as Kd or EC50.
  • Affinity of a binding protein to a ligand such as affinity of an antibody for an epitope can be, for example, from about 100 nanomolar (nM) to about 0. 1 nM, from about 100 nM to about 1 picomolar (pM), or from about 100 nM to about 1 femtomolar (fM).
  • nM nanomolar
  • pM picomolar
  • fM femtomolar
  • the term “avidity” refers to the resistance of a complex of two or more agents to dissociation after dilution.
  • an antibody, or an antigen-binding fragment thereof binds or specifically binds to a human NRP2 polypeptide.
  • NRP2 polypeptides include a human neuropilin-2a (NRP2a) variant 1 (vl) polypeptide, a human NRP2a variant 2 (v2) polypeptide, a human NRP2a variant 3 (v3) polypeptide, a human neuropilin-2b (NRP2b) variant 4 (v4) polypeptide, and a human NRP2b variant 5 (v5) polypeptide.
  • NRP2a human neuropilin-2a
  • vl human neuropilin-2a
  • v2a variant 2 v2a variant 2
  • v3 human NRP2a variant 3
  • v4 human neuropilin-2b
  • v5 human NRP2b variant 5
  • an antibody, or an antigen-binding fragment thereof binds or specifically binds to a human NRP2 polypeptide selected from Table Nl, or a fragment or epitope thereof.
  • an antibody, or an antigen-binding fragment thereof binds or specifically binds a contiguous fragment of about or at least about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, or 50 or more amino acids of a human NRP2 polypeptide selected from Table Nl.
  • the antibody, or antigenbinding fragment thereof binds to a denatured form of the human NRP2 polypeptide.
  • the antibody, or antigen-binding fragment thereof binds to the human NRP2 polypeptide at an epitope that comprises, consists, or consists essentially of residues 642-659 of human NRP2 (SEQ ID NO: 25).
  • the antibody, or antigen-binding fragment thereof binds to the human NRP2 polypeptide with an affinity of about or less than about 10 nM. In some embodiments, the antibody, or antigen-binding fragment thereof, does not substantially bind to cynomolgus NRP2, mouse NRP2, rat NRP2, or human neuropilin-1 (NRP1).
  • the antibody, or antigen-binding fragment thereof binds selectively to a human NRP2 polypeptide relative to a corresponding cynomolgus NRP2, mouse NRP2, rat NRP2, or human NRP1 polypeptide, for instance, wherein its affinity for a human NRP2 polypeptide is significantly stronger than its affinity for a corresponding cynomolgus NRP2, mouse NRP2, rat NRP2, or human NRP 1 polypeptide, for example, by about or at least about 2, 5, 10, 20, 30, 40, 50, 100, 500, or 1000-fold or more.
  • the binding interactions between an antibody, or antigenbinding fragment thereof, and an NRP2 polypeptide can be detected and quantified using a variety of routine methods, including octet and Biacore assays (for example, with appropriately tagged soluble reagents, bound to a sensor chip), FACS analyses with cells expressing a NRP2 polypeptide on the cell surface (either native, or recombinant), immunoassays, fluorescence staining assays, ELISA assays, and microcalorimetry approaches such as ITC (Isothermal Titration Calorimetry). See also the Examples.
  • Antibodies may be prepared by any of a variety of techniques known to those of ordinary skill in the art. See, e.g., Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988. Monoclonal antibodies specific for a polypeptide of interest may be prepared, for example, using the technique of Kohler and Milstein, Eur. J. Immunol. 6:511-519, 1976, and improvements thereto. Also included are methods that utilize transgenic animals such as mice to express human antibodies.
  • Antibodies can also be generated or identified by the use of phage display or yeast display libraries (see, e.g., U.S. Patent No. 7,244,592; Chao et al., Nature Protocols. 1:755-768, 2006).
  • HuCAL Human Combinatorial Antibody Library
  • human libraries designed with human-donor-sourced fragments encoding a light-chain variable region, a heavy-chain CDR-3, synthetic DNA encoding diversity in heavy-chain CDR-1, and synthetic DNA encoding diversity in heavy-chain CDR-2.
  • Other libraries suitable for use will be apparent to persons skilled in the art.
  • antibodies and antigen-binding fragments thereof as described herein include a heavy chain and a light chain CDR set, respectively interposed between a heavy chain and a light chain framework region (FR) set which provide support to the CDRs and define the spatial relationship of the CDRs relative to each other.
  • CDR set refers to the three hypervariable regions of a heavy or light chain V region. Proceeding from the N-terminus of a heavy or light chain, these regions are denoted as “CDR1,” “CDR2,” and “CDR3” respectively.
  • An antigenbinding site therefore, includes six CDRs, comprising the CDR set from each of a heavy and a light chain V region.
  • a polypeptide comprising a single CDR (e.g., a CDR1, CDR2 or CDR3) is referred to herein as a “molecular recognition unit.” Crystallographic analysis of a number of antigen-antibody complexes has demonstrated that the amino acid residues of CDRs form extensive contact with bound antigen, wherein the most extensive antigen contact is with the heavy chain CDR3. Thus, the molecular recognition units are primarily responsible for the specificity of an antigen-binding site.
  • FR set refers to the four flanking amino acid sequences which frame the CDRs of a CDR set of a heavy or light chain V region. Some FR residues may contact bound antigen; however, FRs are primarily responsible for folding the V region into the antigenbinding site, particularly the FR residues directly adjacent to the CDRs. Within FRs, certain amino residues and certain structural features are very highly conserved. In this regard, all V region sequences contain an internal disulfide loop of around 90 amino acid residues. When the V regions fold into a binding-site, the CDRs are displayed as projecting loop motifs which form an antigenbinding surface.
  • immunoglobulin variable domains may be determined by reference to Kabat, E. A. et al., Sequences of Proteins of Immunological Interest. 4th Edition. US Department of Health and Human Services. 1987, and updates thereof.
  • Monoclonal antibodies refer to a homogeneous antibody population wherein the monoclonal antibody is comprised of amino acids (naturally occurring and non-naturally occurring) that are involved in the selective binding of an epitope.
  • Monoclonal antibodies are highly specific, being directed against a single epitope.
  • monoclonal antibody encompasses not only intact monoclonal antibodies and full-length monoclonal antibodies, but also fragments thereof (such as Fab, Fab’, F(ab’)2, Fv), single chain (scFv), variants thereof, fusion proteins comprising an antigen-binding portion, humanized monoclonal antibodies, chimeric monoclonal antibodies, and any other modified configuration of the immunoglobulin molecule that comprises an antigen-binding fragment (epitope recognition site) of the required specificity and the ability to bind to an epitope.
  • fragments thereof such as Fab, Fab’, F(ab’)2, Fv
  • scFv single chain
  • antibody it is not intended to be limited as regards the source of the antibody or the manner in which it is made (e.g., by hybridoma, phage selection, recombinant expression, transgenic animals).
  • the term includes whole immunoglobulins as well as the fragments etc. described above under the definition of “antibody.”
  • an antibody, or an antigen-binding fragment thereof, described herein comprises the light chain constant regions (e.g., CL domain, kappa chain, lambda chain) or heavy chain constant regions (e.g., Fc regions) of any variety of immunoglobulin subtypes (e.g., IgA, IgD, IgE, IgG, IgM, including subclasses and combinations thereof, e.g., IgGl, IgG2, IgG3, IgG4), from any variety of mammals such as mouse, rabbit, or goat.
  • the “Fc region” sequence is usually derived from the heavy chain of an immunoglobulin (Ig) molecule.
  • a typical Ig molecule is composed of two heavy chains and two light chains.
  • the heavy chains can be divided into at least three functional regions: the Fd region, the Fc region (fragment crystallizable region), and the hinge region, the latter being found only in IgG, IgA, and IgD immunoglobulins.
  • the Fd region comprises the variable (VH) and constant (CHI) domains of the heavy chains, and together with the variable (VL) and constant (CL) domains of the light chains forms the antigen-binding fragment or Fab region.
  • the Fc region of IgG, IgA, and IgD immunoglobulins comprises the heavy chain constant domains 2 and 3, designated respectively as CH2 and CH3 regions; and the Fc region of IgE and IgM immunoglobulins comprises the heavy chain constant domains 2, 3, and 4, designated respectively as CH2, CH3, and CH4 regions.
  • the Fc region is mainly responsible for the immunoglobulin effector functions, which include, for example, complement fixation and binding to cognate Fc receptors of effector cells.
  • the hinge region acts as a flexible spacerthat allows the Fab portion to move freely in space relative to the Fc region.
  • the hinge regions are structurally diverse, varying in both sequence and length among immunoglobulin classes and subclasses (see supra).
  • the hinge region may also contain one or more glycosylation site(s), which include a number of structurally distinct types of sites for carbohydrate attachment.
  • IgAl contains five glycosylation sites within a 17 amino acid segment of the hinge region, conferring significant resistance of the hinge region polypeptide to intestinal proteases.
  • Residues in the hinge proximal region of the CH2 domain can also influence the specificity of the interaction between an immunoglobulin and its respective Fc receptor(s) (see, e.g., Shin et al., Intern. Rev. Immunol. 10: 177-186, 1993).
  • Fc region or “Fc fragment” or “Fc” as used herein, thus refers to a portion of an antibody, or antigen-binding fragment thereof, which contains one or more of a CH2 region, a CH3 region, and/or a CH4 region from one or more selected immunoglobulin(s), including fragments and variants and combinations thereof.
  • An “Fc region” may also include one or more hinge region(s) of the heavy chain constant region of an immunoglobulin.
  • the Fc region comprises the CH2 region, CH3 region, CH4 region, and/or hinge region(s) of any one or more immunoglobulin classes, including but not limited to IgA, IgD, IgE, IgG, IgM, including subclasses and combinations thereof.
  • the Fc region is from an IgA immunoglobulin (e.g., mouse, rabbit, goat), including subclasses IgAl and/or IgA2.
  • the Fc region is from an IgD immunoglobulin (e.g., mouse, rabbit, goat).
  • the Fc region is from an IgE immunoglobulin (e.g., mouse, rabbit, goat).
  • the Fc region is from an IgG immunoglobulin (e.g., mouse, rabbit, goat), including subclasses IgGl, IgG2, IgG3, and/or IgG4. In certain embodiments, the Fc region is from an IgM immunoglobulin (e.g., mouse, rabbit, goat).
  • variants refers to a polypeptide or polynucleotide sequence that differs from a reference sequence disclosed herein (e.g., Table SI, Table S2, SEQ ID NOS: 1-8, by one or more substitutions, deletions (e.g., truncations), additions, and/or insertions. Certain variants thus include fragments of a reference sequence described herein. Variant polypeptides are biologically active, that is, they continue to possess the binding activity of a reference polypeptide. Such variants may result from, for example, genetic polymorphism and/or from human manipulation.
  • a biologically active variant will contain one or more conservative substitutions.
  • a “conservative substitution” is one in which an amino acid is substituted for another amino acid that has similar properties, such that one skilled in the art of peptide chemistry would expect the secondary structure and hydropathic nature of the polypeptide to be substantially unchanged.
  • modifications may be made in the structure of the polynucleotides and polypeptides of the present invention and still obtain a functional molecule that encodes a variant or derivative polypeptide with desirable characteristics.
  • one skilled in the art will typically change one or more of the codons of the encoding DNA sequence.
  • amino acids may be substituted for other amino acids in a protein structure without appreciable loss of interactive binding capacity with structures such as, for example, antigen-binding regions of antibodies or binding sites on substrate molecules. Since it is the interactive capacity and nature of a protein that defines that protein’s biological functional activity, certain amino acid sequence substitutions can be made in a protein sequence, and, of course, its underlying DNA coding sequence, and nevertheless obtain a protein with like properties. It is thus contemplated that various changes may be made in the peptide sequences of the disclosed compositions, or corresponding DNA sequences which encode said peptides without appreciable loss of their utility.
  • the hydropathic index of amino acids may be considered.
  • the importance of the hydropathic amino acid index in conferring interactive biologic function on a protein is generally understood in the art (Kyte & Doolittle, 1982, incorporated herein by reference). It is accepted that the relative hydropathic character of the amino acid contributes to the secondary structure of the resultant protein, which in turn defines the interaction of the protein with other molecules, for example, enzymes, substrates, receptors, DNA, antibodies, antigens, and the like.
  • Each amino acid has been assigned a hydropathic index on the basis of its hydrophobicity and charge characteristics (Kyte & Doolittle, 1982).
  • amino acids may be substituted by other amino acids having a similar hydropathic index or score and still result in a protein with similar biological activity, i.e., still obtain a biological functionally equivalent protein.
  • substitution of amino acids whose hydropathic indices are within ⁇ 2 is preferred, those within ⁇ 1 are particularly preferred, and those within ⁇ 0.5 are even more particularly preferred.
  • Patent 4,554,101 the following hydrophilicity values have been assigned to amino acid residues: arginine (+3.0); lysine (+3.0); aspartate (+3.0 ⁇ 1); glutamate (+3.0 ⁇ 1); serine (+0.3); asparagine (+0.2); glutamine (+0.2); glycine (0); threonine (-0.4); proline (-0.5 ⁇ 1); alanine (-0.5); histidine (-0.5); cysteine (-1.0); methionine (-1.3); valine (-1.5); leucine (-1.8); isoleucine (-1.8); tyrosine (-2.3); phenylalanine (-2.5); tryptophan (-3.4).
  • an amino acid can be substituted for another having a similar hydrophilicity value and still obtain a biologically equivalent, and in particular, an immunologically equivalent protein.
  • substitution of amino acids whose hydrophilicity values are within ⁇ 2 is preferred, those within ⁇ 1 are particularly preferred, and those within ⁇ 0.5 are even more particularly preferred.
  • amino acid substitutions are generally therefore based on the relative similarity of the amino acid side-chain substituents, for example, their hydrophobicity, hydrophilicity, charge, size, and the like.
  • Exemplary substitutions that take various of the foregoing characteristics into consideration are well known to those of skill in the art and include: arginine and lysine; glutamate and aspartate; serine and threonine; glutamine and asparagine; and valine, leucine and isoleucine.
  • Amino acid substitutions may further be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity and/or the amphipathic nature of the residues.
  • negatively charged amino acids include aspartic acid and glutamic acid
  • positively charged amino acids include lysine and arginine
  • amino acids with uncharged polar head groups having similar hydrophilicity values include leucine, isoleucine and valine; glycine and alanine; asparagine and glutamine; and serine, threonine, phenylalanine and tyrosine.
  • amino acids that may represent conservative changes include: (1) ala, pro, gly, glu, asp, gin, asn, ser, thr; (2) cys, ser, tyr, thr; (3) val, ile, leu, met, ala, phe; (4) lys, arg, his; and (5) phe, tyr, trp, his.
  • variant polypeptides may also, or alternatively, contain non-conservative changes.
  • variant polypeptides differ from a native or reference sequence by substitution, deletion or addition of about or fewer than about 10, 9, 8, 7, 6, 5, 4, 3, 2 amino acids, or even 1 amino acid.
  • Variants may also (or alternatively) be modified by, for example, the deletion or addition of amino acids that have minimal influence on the immunogenicity, secondary structure, enzymatic activity, and/or hydropathic nature of the polypeptide.
  • variants will display at least about 30%, 40%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% similarity or sequence identity or sequence homology to a reference polypeptide sequence (e.g., Table SI, Table S2, SEQ ID NOs: 1-8).
  • a reference polypeptide sequence e.g., Table SI, Table S2, SEQ ID NOs: 1-8.
  • sequences differing from the reference sequences by the addition e.g., C-terminal addition, N-terminal addition, both
  • deletion, truncation, insertion, or substitution e.g., conservative substitution
  • substitution e.g., conservative substitution
  • variant polypeptides differ from reference sequence by at least one but by less than 10, 9, 8, 7, 6, 5, 4, 3 or 2 amino acid residue(s). In other embodiments, variant polypeptides differ from a reference sequence by at least 1% but less than 10% or 5% of the residues. (If this comparison requires alignment, the sequences should be aligned for maximum similarity. In some instances, “looped” out sequences from deletions or insertions, or mismatches, are considered differences.
  • sequence similarity or sequence identity between sequences are performed as follows. To determine the percent identity of two amino acid sequences, or of two nucleic acid sequences, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes).
  • the length of a reference sequence aligned for comparison purposes is at least 30%, preferably at least 40%, more preferably at least 50%, 60%, and even more preferably at least 70%, 80%, 90%, 100% of the length of the reference sequence.
  • amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position.
  • the percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences.
  • the comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm.
  • the percent identity between two amino acid sequences is determined using the Needleman and Wunsch, (J. Mol. Biol. 48: 444-453, 1970) algorithm which has been incorporated into the GAP program in the GCG software package, using either a Blossum 62 matrix or a PAM250 matrix, and a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a length weight of 1, 2, 3, 4, 5, or 6.
  • the percent identity between two nucleotide sequences is determined using the GAP program in the GCG software package, using a NWSgapdna.CMP matrix and a gap weight of 40, 50, 60, 70, or 80 and a length weight of 1, 2, 3, 4, 5, or 6.
  • a preferred set of parameters includes a Blossum 62 scoring matrix with a gap penalty of 12, a gap extend penalty of 4, and a frameshift gap penalty of 5.
  • the percent identity between two amino acid or nucleotide sequences can be determined using the algorithm of E. Meyers and W. Miller (Cabios. 4: 11-17, 1989) which has been incorporated into the ALIGN program (version 2.0), using a PAM120 weight residue table, a gap length penalty of 12 and a gap penalty of 4.
  • nucleic acid and protein sequences described herein can be used as a “query sequence” to perform a search against public databases to, for example, identify other family members or related sequences.
  • Such searches can be performed using the NBLAST and XBLAST programs (version 2.0) of Altschul, et al., (1990, J. Mol. Biol, 215: 403-10).
  • Gapped BLAST can be utilized as described in Altschul et al., (Nucleic Acids Res. 25: 3389-3402, 1997).
  • the default parameters of the respective programs e.g., XBLAST and NBLAST.
  • polynucleotides and/or polypeptides can be evaluated using a BLAST alignment tool.
  • a local alignment consists simply of a pair of sequence segments, one from each of the sequences being compared.
  • a modification of Smith-Waterman or Sellers algorithms will find all segment pairs whose scores cannot be improved by extension or trimming, called high- scoring segment pairs (HSPs).
  • HSPs high- scoring segment pairs
  • the results of the BLAST alignments include statistical measures to indicate the likelihood that the BLAST score can be expected from chance alone.
  • the raw score, S is calculated from the number of gaps and substitutions associated with each aligned sequence wherein higher similarity scores indicate a more significant alignment. Substitution scores are given by a look-up table (see PAM, BLOSUM).
  • Gap scores are typically calculated as the sum of G, the gap opening penalty and L, the gap extension penalty.
  • the gap cost would be G+Ln.
  • the choice of gap costs, G and L is empirical, but it is customary to choose a high value for G (10-15), e.g., 11, and a low value for L (1-2) e.g., 1.
  • bit score is derived from the raw alignment score S in which the statistical properties of the scoring system used have been taken into account. Bit scores are normalized with respect to the scoring system, therefore they can be used to compare alignment scores from different searches. The terms “bit score” and “similarity score” are used interchangeably. The bit score gives an indication of how good the alignment is; the higher the score, the better the alignment.
  • the E-Value describes the likelihood that a sequence with a similar score will occur in the database by chance. It is a prediction of the number of different alignments with scores equivalent to or better than S that are expected to occur in a database search by chance. The smaller the E-Value, the more significant the alignment. For example, an alignment having an E value of e 117 means that a sequence with a similar score is very unlikely to occur simply by chance. Additionally, the expected score for aligning a random pair of amino acids is required to be negative, otherwise long alignments would tend to have high score independently of whether the segments aligned were related. Additionally, the BLAST algorithm uses an appropriate substitution matrix, nucleotide or amino acid and for gapped alignments uses gap creation and extension penalties. For example, BLAST alignment and comparison of polypeptide sequences are typically done using the BLOSUM62 matrix, a gap existence penalty of 11 and a gap extension penalty of 1.
  • sequence similarity scores are reported from BLAST analyses done using the BLOSUM62 matrix, a gap existence penalty of 11 and a gap extension penalty of 1.
  • sequence identity/similarity scores provided herein refer to the value obtained using GAP Version 10 (GCG, Accelrys, San Diego, Calif.) using the following parameters: % identity and % similarity for a nucleotide sequence using GAP Weight of 50 and Length Weight of 3, and the nwsgapdna.cmp scoring matrix; % identity and % similarity for an amino acid sequence using GAP Weight of 8 and Length Weight of 2, and the BLOSUM62 scoring matrix (Henikoff and Henikoff, PNAS USA. 89: 10915-10919, 1992).
  • GAP uses the algorithm of Needleman and Wunsch (J Mol Biol. 48:443-453, 1970) to find the alignment of two complete sequences that maximizes the number of matches and minimizes the number of gaps.
  • the variant polypeptide comprises an amino acid sequence that can be optimally aligned with a reference polypeptide sequence (see, e.g., Table SI, Table S2, SEQ ID NOs: 1-8) to generate a BLAST bit scores or sequence similarity scores of at least about 50, 60, 70, 80, 90, 100, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460,
  • a reference polypeptide sequence see, e.g., Table SI, Table S2, SEQ ID NOs: 1-28 to generate a BLAST bit scores or sequence similarity scores of at least about 50, 60, 70, 80, 90, 100, 100, 110, 120, 130, 140, 150, 160, 170,
  • a reference polypeptide may be altered in various ways including amino acid substitutions, deletions, truncations, additions, and insertions. Methods for such manipulations are generally known in the art.
  • amino acid sequence variants of a reference polypeptide can be prepared by mutations in the DNA. Methods for mutagenesis and nucleotide sequence alterations are well known in the art. See, for example, Kunkel (PNAS USA. 82: 488-492, 1985); Kunkel et al., (Methods in Enzymol. 154: 367-382, 1987), U.S. Pat. No. 4,873,192, Watson, J. D.
  • REM recursive ensemble mutagenesis
  • the antibody, or antigen-binding fragment thereof is conjugated or covalently attached to a detectable label, for example, to facilitate detection.
  • detectable labels include, without limitation fluorophore/fluore scent dyes, polymer particle labels, metal particle labels, iodine-based labels, alkaline phosphatase, horseradish peroxidase, luminescent labels, radioactive labels or radioisotopes, nanoparticles, and quantum dots.
  • fluorophores or fluorochromes or fluorescent dyes that can be used as directly detectable labels include fluorescein, tetramethylrhodamine, Texas Red, Oregon Green®, and a number of others (e.g., Haugland, Handbook of Fluorescent Probes - 9th Ed., 2002, Molec. Probes, Inc., Eugene OR; Haugland, The Handbook: A Guide to Fluorescent Probes and Labeling Technologies- 10th Ed., 2005, Invitrogen, Carlsbad, CA). Also included are light-emitting or otherwise detectable dyes. The light emitted by the dyes can be visible light or invisible light, such as ultraviolet or infrared light.
  • the dye may be a fluorescence resonance energy transfer (FRET) dye; a xanthene dye, such as fluorescein and rhodamine; a dye that has an amino group in the alpha or beta position (such as a naphthylamine dye, l-dimethylaminonaphthyl-5- sulfonate, l-anilino-8-naphthalende sulfonate and 2-p-touidinyl-6-naphthalene sulfonate); a dye that has 3-phenyl-7-isocyanatocoumarin; an acridine, such as 9-isothiocyanatoacridine and acridine orange; a pyrene, a bensoxadiazole and a stilbene; a dye that has 3-(s-carboxypentyl)-3’-ethyl-5,5’- dimethyloxacarbocyanine (CYA);
  • FRET flu
  • polymer particle labels include micro particles or latex particles of polystyrene, PMMA or silica, which can be embedded with fluorescent dyes, or polymer micelles or capsules which contain dyes, enzymes or substrates.
  • metal particle labels include gold particles and coated gold particles, which can be converted by silver stains.
  • haptens include DNP, fluorescein isothiocyanate (FITC), biotin, and digoxigenin.
  • enzymatic labels include horseradish peroxidase (HRP), alkaline phosphatase (ALP or AP), p-galactosidase (GAL), glucose-6-phosphate dehydrogenase, P-N- acetylglucosamimidase, P-glucuronidase, invertase, Xanthine Oxidase, firefly luciferase and glucose oxidase (GO).
  • HRP horseradish peroxidase
  • ALP or AP alkaline phosphatase
  • GAL p-galactosidase
  • glucose-6-phosphate dehydrogenase P-N- acetylglucosamimidase
  • Examples of commonly used substrates for horseradishperoxidase include 3,3’- diaminobenzidine (DAB), diaminobenzidine with nickel enhancement, 3-amino-9-ethylcarbazole (AEC), Benzidine dihydrochloride (BDHC), Hanker-Yates reagent (HYR), Indophane blue (IB), tetramethylbenzidine (TMB), 4-chloro-l-naphtol (CN), alpha-naphtol pyronin (.alpha.
  • DAB diaminobenzidine
  • AEC 3-amino-9-ethylcarbazole
  • BDHC Benzidine dihydrochloride
  • HMR Hanker-Yates reagent
  • IB Indophane blue
  • TMB tetramethylbenzidine
  • CN 4-chloro-l-naphtol
  • CN alpha-naphtol pyronin
  • Examples of commonly used substrates for alkaline phosphatase include Naphthol-AS-B 1- phosphate/fast red TR (NABP/FR), Naphthol-AS-MX-phosphate/fast red TR (NAMP/FR), Naphthol- AS-B 1 -phosphate/- fast red TR (NABP/FR), Naphthol-AS-MX-phosphate/fast red TR (NAMP/FR), Naphthol-AS-B 1-phosphate/new fuschin (NABP/NF), bromochloroindolyl phosphate/nitroblue tetrazolium (BCIP/NBT), 5-Bromo-4-chloro-3-indolyl-b— d-galactopyranoside (BCIG).
  • NABP/FR Naphthol-AS-B 1- phosphate/fast red TR
  • NAMP/FR Naphthol-AS-MX-phosphate/fast red TR
  • Exemplary iodine-based labels include diatrizoic acid (Hypaque®, GE Healthcare) and its anionic form, diatrizoate.
  • Diatrizoic acid is a radio-contrast agent used in advanced X-ray techniques such as CT scanning. Also included are iodine radioisotopes, described below.
  • luminescent labels include luminol, isoluminol, acridinium esters, 1,2-dioxetanes and pyridopyridazines.
  • electrochemiluminescent labels include ruthenium derivatives
  • radioactive labels include radioactive isotopes of iodide, cobalt, selenium, tritium, carbon, sulfur and phosphorous.
  • radioisotopes that can be used as detectable labels include 32 P, 33 P, 35 S, 3 H, 18 F, 11C, 13 N, 15 O, in In, 169 Yb, "mTC, 55 Fe, and isotopes of iodine such as 123 I, 124 1, 125 I, and 131 E These radioisotopes have different half-lives, types of decay, and levels of energy which can be tailored to match the needs of a particular protocol.
  • Nanoparticles usually range from about 1-1000 nm in size and include diverse chemical structures such as gold and silver particles and quantum dots. When irradiated with angled incident white light, silver or gold nanoparticles ranging from about 40-120 nm will scatter monochromatic light with high intensity. The wavelength of the scattered light is dependent on the size of the particle. Four to five different particles in close proximity will each scatter monochromatic light, which when superimposed will give a specific, unique color. Derivatized nanoparticles such as silver or gold particles can be attached to a broad array of molecules including, proteins, antibodies, small molecules, receptor ligands, and nucleic acids.
  • nanoparticles include metallic nanoparticles and metallic nanoshells such as gold particles, silver particles, copper particles, platinum particles, cadmium particles, composite particles, gold hollow spheres, gold-coated silica nanoshells, and silica-coated gold shells. Also included are silica, latex, polystyrene, polycarbonate, polyacrylate, PVDF nanoparticles, and colored particles of any of these materials.
  • Quantum dots are fluorescing crystals about 1-5 nm in diameter that are excitable by light over a large range of wavelengths. Upon excitation by light having an appropriate wavelength, these crystals emit light, such as monochromatic light, with a wavelength dependent on their chemical composition and size. Quantum dots such as CdSe, ZnSe, InP, or InAs possess unique optical properties; these and similar quantum dots are available from a number of commercial sources (e.g., NN-Labs, Fayetteville, AR; Ocean Nanotech, Fayetteville, AR; Nanoco Technologies, Manchester, UK; Sigma- Aldrich, St. Louis, MO).
  • Detectable labels may be linked to the antibodies described herein or to any other molecule that specifically binds to a biological marker of interest, e.g., an antibody, a nucleic acid probe, or a polymer.
  • detectable labels can also be conjugated to second, and/or third, and/or fourth, and/or fifth binding agents or antibodies, etc.
  • each additional binding agent or antibody used to characterize a biological marker of interest may serve as a signal amplification step.
  • the biological marker may be detected visually using, e.g., light microscopy, fluorescent microscopy, electron microscopy where the detectable substance is for example a dye, a colloidal gold particle, a luminescent reagent.
  • Visually detectable substances bound to a biological marker may also be detected using a spectrophotometer.
  • the detectable substance is a radioactive isotope detection can be visually by autoradiography, or non-visually using a scintillation counter. See, e.g., Larsson, 1988, Immunocytochemistry: Theory and Practice, (CRC Press, Boca Raton, Fla.); Methods in Molecular Biology, vol. 80 1998, John D. Pound (ed.) (Humana Press, Totowa, N.J.).
  • the antibodies, or antigen-binding fragments thereof can be used in any of the compositions, methods, and/or kits described herein.
  • Embodiments of the present invention include methods of using the antibodies, and antigenbinding fragments thereof, described herein to determine the presence, absence, amount, levels, and/or subcellular localization of an NRP2 polypeptide in a biological sample, such as a biological sample.
  • Such methods include, for example, the use of the antibodies, or antigen-binding fragments thereof, as a companion diagnostic to identify a subject for NRP2 -targeted therapy, including for the administration of at least one NRP2-targeted therapeutic agent.
  • the subject is considered suitable for NRP2 -targeted therapy if the amount of NRP2 polypeptide in a biological sample is increased relative to a control.
  • the subject is considered suitable for NRP2 -targeted therapy if the subcellular localization of the NRP2 polypeptide is increased relative to a control, for example, subcellular localization to the nucleus or nuclear envelope.
  • the methods include using the antibodies, or antigen-binding fragment thereof, as a companion diagnostic to identify a subject having or suspected of having a cancer or tumor that expresses or over-expresses an NRP2 polypeptide, and optionally for treating or causing the subject to be treated with an NRP2 -targeted therapy.
  • Certain embodiments relate generally to methods of determining an amount of a human NRP2 polypeptide in a biological sample, comprising (a) contacting the biological sample with an antibody, or antigen-binding fragment thereof, as described herein; and (b) determining the amount of the antibody, or antigen-binding fragment thereof, in the biological sample, which thereby determines the amount of the human NRP2 polypeptide in the biological sample.
  • the sample is denatured prior to or during step (a) of the methods.
  • Also included are methods of identifying an NRP2-expressing cancer in a biological sample of cancer tissue from a subject comprising (a) contacting the biological sample with an antibody, or antigen-binding fragment thereof, as described herein; and (b) determining the amount or subcellular localization of the antibody, or antigen-binding fragment thereof, in the biological sample, which thereby determines the amount or subcellular localization of NRP2 in the biological sample; and (c) identifying the NRP2 -expressing cancer if (i) the amount of NRP2 in the biological sample of cancer tissue from the subject is increased relative to a control or reference or (ii) the subcellular localization of the NRP2 is increased relative to a control or reference.
  • the increase in subcellular localization is to the nucleus or nuclear envelope. That is, in specific embodiments, the subcellular localization of the NRP2 is increased in the nucleus or nuclear envelope relative to the control or reference.
  • (b) comprises determining the ratio of NRP2 localized in the nucleus or nuclear envelope (nuclear NRP2) relative to NRP2 localized on the cell surface (cell surface NRP2), and (c) comprises identifying the NRP2 -expressing cancer if the ratio of nuclear NRP2/cell surface NRP2 is increased relative to a control or reference.
  • Some embodiments include administering or causing to be administered to the subject having the NRP2 -expressing cancer of (c) at least one NRP2-targeted therapeutic agent, for example, a therapeutic antibody, or antigen-binding fragment thereof, which binds to human NRP2, either as a standalone agent or in combination with at least one additional anti-cancer therapy or agent such as one or more chemotherapeutic agents.
  • at least one NRP2-targeted therapeutic agent for example, a therapeutic antibody, or antigen-binding fragment thereof, which binds to human NRP2, either as a standalone agent or in combination with at least one additional anti-cancer therapy or agent such as one or more chemotherapeutic agents.
  • Also included are methods of identifying a subject for NRP2-targeted therapy comprising (a) contacting a biological sample from the subject with an antibody, or antigen-binding fragment thereof, as described herein; (b) determining the amount or subcellular localization of the antibody, or antigenbinding fragment thereof, in the biological sample, which determines the amount or subcellular localization of NRP2 in the sample; and (c) identifying the subject as suitable for NRP2 -targeted therapy if (i) the amount of the NRP2 in the biological sample is increased relative to a control or reference, or (ii) the subcellular localization of the NRP2 is increased relative to a control or reference.
  • step (b) comprises determining the ratio of NRP2 localized in the nucleus or nuclear envelope (nuclear NRP2) relative to NRP2 localized on the cell surface (cell surface NRP2), and (c) comprises identifying the NRP2- expressing cancer if the ratio of nuclear NRP2/cell surface NRP2 is increased relative to a control or reference.
  • Some embodiments include administering or causing to be administered to the subject of (c) at least one NRP2 -targeted therapeutic agent, either as a standalone therapeutic or in combination with one or more additional therapeutic agents, for example, anti -cancer agents.
  • CRPC castrationresistant prostate cancer
  • AR androgen receptor
  • a patient that is “refractory” to AR- targeted therapy does not significantly respond to, has previously failed to respond to, or has become non-responsive (e.g., via selection) to the AR-targeted therapy
  • increased nuclear localization of (sumoylated) NRP2 promotes castration-resistant prostate cancer (CRPC)- specific gene expression by stabilizing a complex between the androgen receptor (AR) and nuclear pore proteins (see, for example, Dutta et al., Oncogene. 41: 3747-3760, 2022).
  • Such subjects are typically considered suitable for a more aggressive treatment regimen than AR-targeted therapy, for example, an aggressive treatment regimen that includes one or more chemotherapeutic agents.
  • Certain of these and related embodiments thus comprise (a) contacting a biological sample from the subject with an antibody, or antigen-binding fragment thereof, as described herein; (b) determining the subcellular localization of the antibody, or antigen-binding fragment thereof, in the biological sample, which determines the subcellular localization of NRP2 in the sample; and (c) identifying the subject as being suitable for an aggressive treatment regimen if the subcellular localization of the NRP2 in the nucleus or nuclear envelope is increased relative to a control or reference.
  • (b) comprises determining the ratio of NRP2 localized in the nucleus or nuclear envelope (nuclear NRP2) relative to NRP2 localized on the cell surface (cell surface NRP2), and (c) comprises identifying the subject as being suitable for the aggressive treatment regimen if the ratio of nuclear NRP2/cell surface NRP2 is increased relative to a control or reference.
  • the aggressive treatment regimen comprises at least one NRP2 -targeted therapeutic agent, for example, a therapeutic antibody, or antigen-binding fragment thereof, which binds to human NRP2, in combination with at least one chemotherapeutic agent, including DNA damaging agents.
  • Also included are more general methods of identifying NRP2-mediated drug resistance in a subject comprising (a) contacting a biological sample from the subject with an antibody, or antigenbinding fragment thereof, as described herein; (b) determining the subcellular localization of the antibody, or antigen-binding fragment thereof, in the biological sample, which determines the subcellular localization of NRP2 in the sample; and (c) identifying the subject as having NRP2- mediated drug resistance if the subcellular localization of NRP2 to the nucleus or nuclear envelope is increased relative to a control or reference.
  • Some embodiments include administering or causing to be administered to the subject of (c) at least one NRP2-targeted therapeutic agent, optionally a therapeutic antibody, or antigen-binding fragment thereof, which binds to human NRP2, optionally in combination with at least one additional anti-cancer therapy or agent, optionally radiotherapies, cancer immunotherapies, chemotherapeutic agents (optionally DNA damaging agents, DNA repair inhibitors), hormonal therapeutic agents, kinase inhibitors, anti-growth factor therapies, and androgen receptor (AR)-targeted therapies.
  • (c) comprises correlating a higher increase in subcellular localization of NRP2 to the nucleus or nuclear envelope with a more advanced stage of NRP2 -mediated drug resistance.
  • the NRP2 -targeted therapeutic agent is a therapeutic antibody, or antigen-binding fragment thereof, which binds to human NRP2. Examples of such agents are described in WO 2019/195770 and WO 2021/067761.
  • the NRP2-targeted therapeutic agent is a small molecule inhibitor of NRP2. Examples of such agents include benzamidine-based NRP2 inhibitors (see, for example, Said et al., Bioorg Chem. 100: 103856, 2020), and others.
  • additional anti-cancer therapies and agents include radiotherapies, cancer immunotherapies or immunotherapy agents (e.g., immune checkpoint modulatory agents, cancer vaccines, oncolytic viruses, cytokines, cell-based immunotherapies), chemotherapeutic agents (for example, DNA damaging agents, DNA repair inhibitors), hormonal therapeutic agents (e.g., hormonal agonists, hormonal antagonists), kinase inhibitors, anti-growth factor therapies, and androgen receptor (AR)-targeted therapies.
  • radiotherapies e.g., cancer immunotherapies or immunotherapy agents
  • cancer vaccines e.g., oncolytic viruses, cytokines, cell-based immunotherapies
  • chemotherapeutic agents for example, DNA damaging agents, DNA repair inhibitors
  • hormonal therapeutic agents e.g., hormonal agonists, hormonal antagonists
  • kinase inhibitors e.g., anti-growth factor therapies, and androgen receptor (AR)-targeted therapies.
  • AR androgen receptor
  • the at least one chemotherapeutic agent is selected from one or more of an alkylating agent, an anti-metabolite, a cytotoxic antibiotic, a topoisomerase inhibitor (type 1 or type II), and an anti-microtubule agent.
  • the alkylating agent is selected from one or more of nitrogen mustards (optionally mechlorethamine, cyclophosphamide, mustine, melphalan, chlorambucil, ifosfamide , and busulfan), nitrosoureas (optionally N-Nitroso-N-methylurea (MNU), carmustine (BCNU), lomustine (CCNU), semustine (MeCCNU), fotemustine, and streptozotocin), tetrazines (optionally dacarbazine, mitozolomide, and temozolomide), aziridines (optionally thiotepa, mytomycin, and diaziquone (AZQ)), cisplatins and derivatives thereof (optionally carboplatin and oxaliplatin), and non-classical alkylating agents (optionally procarbazine and hexamethylmelamine); the anti-metabolite is selected from one or more of anti-fo
  • the at least one hormonal therapeutic agent is a hormonal agonist or a hormonal antagonist.
  • the hormonal agonist is selected from one or more of a progestogen (progestin), a corticosteroid (optionally prednisolone, methylprednisolone, or dexamethasone), insulin like growth factors, VEGF derived angiogenic and lymphangiogenic factors (optionally VEGF-A, VEGF-A145, VEGF-A165, VEGF-C, VEGF-D, PIGF-2), fibroblast growth factor (FGF), galectin, hepatocyte growth factor (HGF), platelet derived growth factor (PDGF), transforming growth factor (TGF)-beta, an androgen, an estrogen, and a somatostatin analog.
  • progestogen progestin
  • corticosteroid optionally prednisolone, methylprednisolone, or dexamethasone
  • insulin like growth factors VEGF
  • the hormonal antagonist is selected from one or more of a hormone synthesis inhibitor, optionally an aromatase inhibitor or a gonadotropin-releasing hormone (GnRH) or an analog thereof, and a hormone receptor antagonist, optionally a selective estrogen receptor modulator (SERM) or an anti-androgen, or an antibody directed against a hormonal receptor, optionally cixutumumab, dalotuzumab, figitumumab, ganitumab, istiratumab, robatumumab, alacizumab pegol, bevacizumab, icrucumab, ramucirumab, fresolimumab, metelimumab, naxitamab, cetuximab, depatuxizumab mafodotin, futuximab, imgatuzumab, laprituximab emtansine, matuzumab, modotuximab, necitumuma
  • the kinase inhibitor is selected from one or more of adavosertib, afanitib, aflibercept, axitinib, bevacizumab, bosutinib, cabozantinib, cetuximab, cobimetinib, crizotinib, dasatinib, entrectinib, erdafitinib, erlotinib, fostamitinib, gefitinib, ibrutinib, imatinib, lapatinib, lenvatinib, mubritinib, nilotinib, panitumumab, pazopanib, pegaptanib, ponatinib, ranibizumab, regorafenib, ruxolitinib, sorafenib, sunitinib, SU6656, tofacitinib
  • anti-cancer agents include PD-L1 inhibitors, PD-1 inhibitors, EGFR inhibitors, VEGF/VEGFR inhibitors, and androgen receptor (AR)-targeted therapies, including androgen deprivation therapies.
  • PD-L1 inhibitors include atezolizumab, avelumab, and durvalumab
  • examples of PD-1 inhibitors include nivolumab, pembrolizumab, cemiplimab, dostarlimab, and retifanlimab
  • examples of EGFR inhibitors include cetuximab, dacomitinib, erlotinib, gefitinib, lapatinib, mobocertinib, necitumumab, neratinib, osimertinib, panitumumab, and vandetanib
  • examples of VEGF/VEGFR inhibitors include aflibercept, axitinib, bevacizum
  • AR-targeted therapies include steroidal antiandrogens (SAAs) such as abiraterone acetate, allylestrenol, chlormadinone acetate, cyproterone acetate, delmadinone acetate, gestonorone caproate, hydroxyprogesterone caproate, medroxyprogesterone acetate, megestrol acetate, osaterone acetate, oxendolone, and spironolactone; and nonsteroidal antiandrogens (NSAAs) such as aminoglutethimide, apalutamide, bicalutamide, enzalutamide, flutamide, ketoconazole, nilutamide, and topilutamide.
  • SAAs steroidal antiandrogens
  • NSAAs nonsteroidal antiandrogens
  • Certain embodiments comprise first obtaining the biological sample from a subject, for example, by receiving the biological sample from a healthcare provider, including wherein the subject has or is suspected of having an NRP2 -associated disease, or a cancer.
  • step (a) comprises receiving the biological sample from a healthcare provider, such as a physician, clinic, or hospital.
  • the entity receiving the biological sample and/or performing the testing can be associated with or separate from the healthcare provider.
  • the entity receiving the sample and/or performing the testing is a third party diagnostic company.
  • the entity receiving the sample and/or performing the testing is a clinical or hospital-associated diagnostic laboratory.
  • the method comprises providing information to the same or different healthcare provider (e.g., physician) on the presence, absence, amount, levels, or subcellular localization of the NRP2 polypeptide in the biological sample.
  • the information on the subcellular localization of NRP2 comprises a ratio of nuclear NRP2/cell surface NRP2 in the biological sample.
  • NRP2-associated disease or condition refers to diseases and conditions in which NRP2 activity, expression, and/or spatial distribution plays a role in the pathophysiology of that disease or condition.
  • NRP2-associated diseases and conditions include cancer and diseases or pathologies associated with cancer including cancer cell growth, cancer initiation, cancer migration, cancer cell adhesion, invasion, chemoresistance, and metastasis.
  • NRP2 -associated diseases and conditions include inflammatory diseases or conditions such as rheumatoid arthritis (RA), osteoarthritis (OA), and inflammatory lung diseases (ILDs) such as sarcoidosis, scleroderma, chronic obstructive pulmonary disorder (COPD), and pulmonary fibrosis.
  • inflammatory diseases or conditions such as rheumatoid arthritis (RA), osteoarthritis (OA), and inflammatory lung diseases (ILDs) such as sarcoidosis, scleroderma, chronic obstructive pulmonary disorder (COPD), and pulmonary fibrosis.
  • IPD inflammatory lung diseases
  • Additional examples include diseases associated with lymphatic development, lymphangiogenesis, and lymphatic damage, including edema, lymphedema, secondary lymphedema, inappropriate fat absorption and deposition, excess fat deposition, and vascular permeability.
  • diseases associated with infections including latent infections, and diseases associated with allergic disorders/diseases and allergic responses, including neutrophilic asthma, antineutrophil cytoplasmic antibody (ANCA)-associated systemic vasculitis, systemic lupus erythematosus, inflammasome- related disease(s), and skin-related neutrophil-mediated disease(s) such as pyoderma gangrenosum.
  • neutrophilic asthma antineutrophil cytoplasmic antibody (ANCA)-associated systemic vasculitis, systemic lupus erythematosus, inflammasome- related disease(s), and skin-related neutrophil-mediated disease(s) such as pyoderma gangrenosum.
  • ANCA antineutrophil cytoplasmic antibody
  • Additional examples include diseases associated with granulomatous inflammatory diseases including sarcoidosis and granulomas, and fibrotic diseases including endometriosis, fibrosis, endothelial to mesenchymal transition (EM
  • diseases associated with inappropriate smooth muscle contractility, smooth muscle compensation and decompensation, vascular smooth muscle cell migration and/or adhesion, and diseases associated with inappropriate autophagy, phagocytosis, and efferocytosis are also included.
  • diseases associated with inappropriate migratory cell movement as described herein. Additional examples include neuronal diseases, including diseases associated with peripheral nervous system remodeling and pain perception.
  • diseases associated with bone development and/or bone remodeling are also included.
  • the term “inappropriate” refers to an activity or characteristic that associates with or causes a pathology or disease state.
  • the biological sample can include any variety of samples, fluids, or tissues.
  • Non-limiting examples of biological samples include blood, plasma, skin, hair, hair follicles, saliva, oral mucous, vaginal mucous, sweat, tears, epithelial tissues, urine, semen, seminal fluid, seminal plasma, prostatic fluid, excreta, biopsy, ascites, cerebrospinal fluid, synovial fluid, bronchoalveolar lavage (BALF), lymph, tissue extracts sample, and biopsy samples, such as cancer or tumor biopsy sample, or a suspected cancer or tumor biopsy sample.
  • blood, plasma, skin, hair, hair follicles saliva, oral mucous, vaginal mucous, sweat, tears, epithelial tissues, urine, semen, seminal fluid, seminal plasma, prostatic fluid, excreta, biopsy, ascites, cerebrospinal fluid, synovial fluid, bronchoalveolar lavage (BALF), lymph, tissue extracts sample, and biopsy samples, such as cancer or tumor biopsy sample, or a suspected cancer or tumor biopsy sample.
  • the biological sample is a biopsy sample, including wherein the biopsy sample is a cancer or suspected cancer biopsy sample.
  • the biopsy sample is selected from skin tissue, liver tissue, pancreatic tissue, prostate tissue, mesothelial tissue, epithelial tissue, ovarian tissue, colorectal tissue, gastric tissue, brain tissue, lung tissue, kidney tissue, bladder tissue, uterine tissue, esophageal tissue, cervical tissue, testicular tissue, breast tissue, and mesenchymal tissue such as bone tissue, cartilage tissue, fat tissue, muscle tissue, vascular tissue, blood, or hematopoietic cells/tissue, for example, a liquid biopsy.
  • control or reference is a reference standard, a biological sample from a healthy subject, or a healthy biological sample from the same subject.
  • control is a non-cancerous biological sample from the same subject, for example, of the same tissue type.
  • the presence, absence, amount, levels, or cellular localization (e.g., surface, subcellular) of an antibody, or an antigen-binding fragment thereof, and thus an NRP2 polypeptide in a biological sample can be measured according to any variety of techniques in the art. For instance, certain embodiments may employ standard methodologies and detectors. Examples include immunohistochemistry (IHC), immunofluorescence (IF), Western blotting, immunoprecipitation, enzyme-linked immunosorbent assays (ELISA), slot blotting, and peptide mass fingerprinting. Certain embodiments may employ cell-sorting or cell visualization or imaging devices/techniques to visualize, detect, and/or quantitate the amount or levels of an antibody, or antigen-binding fragment thereof. Examples include flow cytometry (or FACS), immunofluorescence analysis (IF A), and in situ hybridization techniques, such as fluorescent in situ hybridization (FISH).
  • FACS flow cytometry
  • IF A immunofluorescence analysis
  • FISH fluorescent in situ hybridization
  • IHC or IF analysis examples include the use of IHC or IF analysis.
  • IH chromogenic immunohistochemistry
  • the anti-NRP2 antibody is conjugated to an enzyme, such as peroxidase (immunoperoxidase), which catalyzes a color-producing reaction (see, for example, Ramos-Vara, “Technical Aspects of Immunohistochemistry”. Veterinary Pathol. 42: 405- 426, 2005).
  • the antibody is labeled directly or indirectly with a fluorophore, such as fluorescein or rhodamine, which allows visualization by light microscopy with a fluorescent microscope.
  • Certain embodiments employ primary (or direct) IF analysis, wherein the primary anti- NRP2 antibody is chemically linked to a fluorophore. Certain embodiments employ secondary (or indirect) IF analysis, which requires at least two antibodies; the unlabeled primary anti-NRP2 antibody specifically binds the target molecule, and one or more secondary antibodies, which carries the fluorophore(s), bind to the primary antibody.
  • steps (a) and/or (b) of the methods provided herein comprise performing an IHC or IF assay on the biological sample.
  • Some embodiments include the step(s) of preparing the biological sample, for example, by any combination of tissue collection, fixation (e.g., formalin), embedding in a medium such as paraffin wax or cryomedia, and sectioning with an instrument such as a microtome, cryostat, or vibratome (for example, to a size range of about 3-5 pm).
  • Certain embodiments include the step(s) of mounting the sample (e.g., slices) on slides, dehydrating the sample using alcohol washes of increasing concentrations (e.g., 50%, 75%, 90%, 95%, 100%), and clearing the sample using a detergent (e.g., xylene), and imaging under a microscope.
  • Certain embodiments include the additional pre-antibody treatment steps of deparaffinization and antigen retrieval. For instance, for certain formalin-fixed paraffin-embedded tissues, antigen-retrieval includes pre-treating the sections with heat or protease. Also included are any appropriate wash steps.
  • Particular embodiments include the step of imaging or visualizing the treated biological sample for the presence, absence, levels, amount, or localization (e.g., surface, subcellular) of the labeled/stained anti-NRP2 antibody, as described herein.
  • the IHC or IF assay comprises a multiplex IHC or IF assay (see, for example, Tan, Wei Chang Colin et al. “Overview of multiplex immunohistochemistry/ immunofluorescence techniques in the era of cancer immunotherapy.” Cancer communications (London, England) vol. 40,4 (2020): 135-153).
  • Multiplex IHC or IF includes contacting the biological sample with at least one additional antibody, or antigen-binding fragment thereof, which specifically binds to an additional marker of interest, which has or utilizes a different (direct or indirect) detectable label.
  • the additional marker of interest is selected from one or more of signal transduction pathway molecules (for example, VEGF-C, VEGF-A, EGF, IGF, FGF, TGF-beta, VEGFR1, VEGFR2, VEGFR3, CCR7, EGFR1, EGFR2, PDGFR, TGFR1, TGFR2, TGFR3, c-MET); EMT markers such as mesenchymal markers (for example, N-cadherin, E-cadherin, OB-cadherin, ZO-1, a5pi integrin 1, aVp6 integrin, Syndecan-1, FSP1, Cytokeratin, a-SMA, Vimentin 1, P- Catenin), epithelial markers (for example, CDH1, EPCAM, claudins, and cytokeratins), and related transcription factors (for example, Snail, Slug, ZEB1, ZEB2, and Twist); lymphangiogenesis markers (for example, lymphatic signal transduction pathway
  • Computer software products or method typically include or use computer readable medium having computer-executable instructions for performing the logic steps of the method.
  • the computer executable instructions may be written in a suitable computer language or combination of several languages.
  • Certain embodiments include methods and related compositions for expressing and purifying an anti-NRP2 antibody or other polypeptide-based agent described herein.
  • Such recombinant anti- NRP2 antibodies can be conveniently prepared using standard protocols as described for example in Sambrook, et al., (1989, supra), in particular Sections 16 and 17; Ausubel et al., (1994, supra), in particular Chapters 10 and 16; and Coligan et al., Current Protocols in Protein Science (John Wiley & Sons, Inc. 1995-1997), in particular Chapters 1, 5 and 6.
  • anti-NRP2 antibodies may be prepared by a procedure including one or more of the steps of: (a) preparing a construct comprising a polynucleotide sequences that encode an anti-NRP2 antibody heavy and light chain and that are operably linked to a regulatory element; (b) introducing the constructs into a host cell; (c) culturing the host cell to express an anti-NRP2 antibody; and (d) isolating an anti-NRP2 antibody from the host cell.
  • Anti-NRP2 antibody polynucleotides are described elsewhere herein.
  • a nucleotide sequence encoding an anti-NRP2 antibody, or a functional equivalent may be inserted into appropriate expression vector, i.e., a vector which contains the necessary elements for the transcription and translation of the inserted coding sequence.
  • appropriate expression vector i.e., a vector which contains the necessary elements for the transcription and translation of the inserted coding sequence.
  • Methods which are well known to those skilled in the art may be used to construct expression vectors containing sequences encoding a polypeptide of interest and appropriate transcriptional and translational control elements. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. Such techniques are described in Sambrook et al., Molecular Cloning, A Laboratory Manual (1989), and Ausubel et al., Current Protocols in Molecular Biology (1989).
  • a variety of expression vector/host systems are known and may be utilized to contain and express polynucleotide sequences. These include, but are not limited to, microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems infected with virus expression vectors (e.g., baculovirus); plant cell systems transformed with virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or with bacterial expression vectors (e.g., Ti or pBR322 plasmids); or animal cell systems, including mammalian cell and more specifically human cell systems.
  • microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors
  • yeast transformed with yeast expression vectors insect cell systems infected with virus expression vectors (e.g., baculovirus)
  • control elements or “regulatory sequences” present in an expression vector are those non-translated regions of the vector— enhancers, promoters, 5 ’ and 3 ’ untranslated regions— which interact with host cellular proteins to carry out transcription and translation. Such elements may vary in their strength and specificity. Depending on the vector system and host utilized, any number of suitable transcription and translation elements, including constitutive and inducible promoters, may be used. For example, when cloning in bacterial systems, inducible promoters such as the hybrid lacZ promoter of the PBLUESCRIPT phagemid (Stratagene, La Jolla, Calif.) or PSPORT1 plasmid (Gibco BRL, Gaithersburg, Md.) and the like may be used.
  • inducible promoters such as the hybrid lacZ promoter of the PBLUESCRIPT phagemid (Stratagene, La Jolla, Calif.) or PSPORT1 plasmid (Gibco BRL, Gaithersburg, Md.
  • promoters from mammalian genes or from mammalian viruses are generally preferred. If it is necessary to generate a cell line that contains multiple copies of the sequence encoding a polypeptide, vectors based on SV40 or EBV may be advantageously used with an appropriate selectable marker.
  • a number of expression vectors may be selected depending upon the use intended for the expressed polypeptide. For example, when large quantities are needed, vectors which direct high level expression of fusion proteins that are readily purified may be used.
  • vectors include, but are not limited to, the multifunctional E. coli cloning and expression vectors such as BLUESCRIPT (Stratagene), in which the sequence encoding the polypeptide of interest may be ligated into the vector in frame with sequences for the amino-terminal Met and the subsequent 7 residues of p-galactosidase so that a hybrid protein is produced; pIN vectors (Van Heeke & Schuster, J. Biol. Chem.
  • pGEX Vectors may also be used to express foreign polypeptides as fusion proteins with glutathione S-transferase (GST).
  • GST glutathione S-transferase
  • fusion proteins are soluble and can easily be purified from lysed cells by adsorption to glutathione-agarose beads followed by elution in the presence of free glutathione.
  • Proteins made in such systems may be designed to include heparin, thrombin, or factor XA protease cleavage sites so that the cloned polypeptide of interest can be released from the GST moiety at will.
  • Certain embodiments may employ E. coli-based expression systems (see, e.g., Structural Genomics Consortium et al., Nature Methods. 5: 135-146, 2008). These and related embodiments may rely partially or totally on ligation-independent cloning (LIC) to produce a suitable expression vector.
  • protein expression may be controlled by a T7 RNA polymerase (e.g., pET vector series).
  • T7 RNA polymerase e.g., pET vector series
  • These and related embodiments may utilize the expression host strain BL21(DE3), a XDE3 lysogen of BL21 that supports T7 -mediated expression and is deficient in Ion and ompT proteases for improved target protein stability.
  • expression host strains carrying plasmids encoding tRNAs rarely used in E. coli such as ROSETTATM (DE3) and Rosetta 2 (DE3) strains.
  • Cell lysis and sample handling may also be improved using reagents sold under the trademarks BENZONASE® nuclease and BUGBUSTER® Protein Extraction Reagent.
  • BENZONASE® nuclease and BUGBUSTER® Protein Extraction Reagent.
  • auto-inducing media can improve the efficiency of many expression systems, including high- throughput expression systems.
  • Media of this type e.g., OVERNIGHT EXPRESSTM Autoinduction System gradually elicit protein expression through metabolic shift without the addition of artificial inducing agents such as IPTG.
  • Particular embodiments employ hexahistidine tags (such as those sold under the trademark HIS*TAG® fusions), followed by immobilized metal affinity chromatography (IMAC) purification, or related techniques.
  • clinical grade proteins can be isolated from E. coli inclusion bodies, without or without the use of affinity tags (see, e.g., Shimp et al., Protein Expr Purif. 50:58-67, 2006).
  • affinity tags see, e.g., Shimp et al., Protein Expr Purif. 50:58-67, 2006.
  • certain embodiments may employ a cold-shock induced E. coli high-yield production system, because over-expression of proteins in Escherichia coli at low temperature improves their solubility and stability (see, e.g., Qing et al., Nature Biotechnology. 22:877-882, 2004).
  • high-density bacterial fermentation systems For example, high cell density cultivation of Ralstonia eutropha allows protein production at cell densities of over 150 g/L, and the expression of recombinant proteins at titers exceeding 10 g/L.
  • yeast Saccharomyces cerevisiae a number of vectors containing constitutive or inducible promoters such as alpha factor, alcohol oxidase, and PGH may be used.
  • constitutive or inducible promoters such as alpha factor, alcohol oxidase, and PGH
  • PGH palladium phosphate
  • Pichia pandoris expression systems see, e.g., Li et al., Nature Biotechnology. 24, 210 - 215, 2006; and Hamilton et al., Science, 301: 1244, 2003).
  • yeast systems that are engineered to selectively glycosylate proteins, including yeast that have humanized N-glycosylation pathways, among others (see, e.g., Hamilton et al., Science. 313: 1441-1443, 2006; Wildt et al., Nature Reviews Microbiol. 3: 119-28, 2005; and Gemgross et al., Nature-Biotechnology. 22: 1409 -1414, 2004; U.S. Patent Nos. 7,629,163; 7,326,681; and 7,029,872).
  • recombinant yeast cultures can be grown in Fembach Flasks or 15L, 50L, 100L, and 200L fermentors, among others.
  • sequences encoding polypeptides may be driven by any of a number of promoters.
  • viral promoters such as the 35 S and 19S promoters of CaMV may be used alone or in combination with the omega leader sequence from TMV (Takamatsu, EMBO J. 3:17-311 (1987)).
  • plant promoters such as the small subunit of RUBISCO or heat shock promoters may be used (Coruzzi et al., EMBO J. 3: 1671-1680 (1984); Broglie et al., Science 224:838-843 (1984); and Winter et al., Results Probl. Cell Differ. 17:85-105 (1991)).
  • constructs can be introduced into plant cells by direct DNA transformation or pathogen-mediated transfection. Such techniques are described in a number of generally available reviews (see, e.g., Hobbs in McGraw Hill, Yearbook of Science and Technology, pp. 191-196 (1992)).
  • An insect system may also be used to express a polypeptide of interest.
  • Autographa califomica nuclear polyhedrosis vims (AcNPV) is used as a vector to express foreign genes in Spodoptera frugiperda cells or in Trichoplusia cells.
  • the sequences encoding the polypeptide may be cloned into a non-essential region of the virus, such as the polyhedrin gene, and placed under control of the polyhedrin promoter. Successful insertion of the polypeptide-encoding sequence will render the polyhedrin gene inactive and produce recombinant virus lacking coat protein.
  • the recombinant viruses may then be used to infect, for example, S.
  • frugiperda cells or Trichoplusia cells in which the polypeptide of interest may be expressed (Engelhard et al., PNAS. U.S.A. 91:3224- 3227 (1994)). Also included are baculovirus expression systems, including those that utilize SF9, SF21, and T. ni cells (see, e.g., Murphy and Piwnica-Worms, Curr Protoc Protein Sci. Chapter 5:Unit5.4, 2001). Insect systems can provide post-translation modifications that are similar to mammalian systems.
  • a number of viral-based expression systems are generally available.
  • sequences encoding a polypeptide of interest may be ligated into an adenovirus transcription/translation complex consisting of the late promoter and tripartite leader sequence. Insertion in a non-essential El or E3 region of the viral genome may be used to obtain a viable virus which is capable of expressing the polypeptide in infected host cells (Logan & Shenk, Proc. Natl. Acad. Sci. U.S.A. 81:3655-3659 (1984)).
  • transcription enhancers such as the Rous sarcoma virus (RSV) enhancer, may be used to increase expression in mammalian host cells.
  • RSV Rous sarcoma virus
  • Examples of useful mammalian host cell lines include monkey kidney CV1 line transformed by SV40 (COS-7, ATCC CRL 1651); human embryonic kidney line (293 or 293 cells sub-cloned for growth in suspension culture, Graham et al., J. Gen Virol. 36:59 (1977)); baby hamster kidney cells (BHK, ATCC CCL 10); mouse sertoli cells (TM4, Mather, Biol. Reprod.
  • COS-7 monkey kidney CV1 line transformed by SV40
  • human embryonic kidney line (293 or 293 cells sub-cloned for growth in suspension culture, Graham et al., J. Gen Virol. 36:59 (1977)
  • baby hamster kidney cells BHK, ATCC CCL 10
  • mouse sertoli cells TM4, Mather, Biol. Reprod.
  • monkey kidney cells (CV1 ATCC CCL 70); African green monkey kidney cells (VERO-76, ATCC CRL- 1587); human cervical carcinoma cells (HELA, ATCC CCL 2); canine kidney cells (MDCK, ATCC CCL 34); buffalo rat liver cells (BRL 3A, ATCC CRL 1442); human lung cells (W138, ATCC CCL 75); human liver cells (Hep G2, HB 8065); mouse mammary tumor (MMT 060562, ATCC CCL51); TRI cells (Mather et al., Annals N.Y. Acad. Sci. 383:44-68 (1982)); MRC 5 cells; FS4 cells; and a human hepatoma line (Hep G2).
  • CHO Chinese hamster ovary
  • DHFR-CHO cells Urlaub et al., PNAS USA 77:4216 (1980)
  • myeloma cell lines such as NSO and Sp2/0.
  • CHO Chinese hamster ovary
  • myeloma cell lines such as NSO and Sp2/0.
  • Certain preferred mammalian cell expression systems include CHO and HEK293-cell based expression systems.
  • Mammalian expression systems can utilize attached cell lines, for example, in T-flasks, roller bottles, or cell factories, or suspension cultures, for example, in IL and 5L spinners, 5L, 14L, 40L, 100L and 200L stir tank bioreactors, or 20/50L and 100/200L WAVE bioreactors, among others known in the art. Also included is the cell-free expression of proteins. These and related embodiments typically utilize purified RNA polymerase, ribosomes, tRNA and ribonucleotides; these reagents may be produced by extraction from cells or from a cell-based expression system.
  • Specific initiation signals may also be used to achieve more efficient translation of sequences encoding a polypeptide of interest. Such signals include the ATG initiation codon and adjacent sequences. In cases where sequences encoding the polypeptide, its initiation codon, and upstream sequences are inserted into the appropriate expression vector, no additional transcriptional or translational control signals may be needed. However, in cases where only coding sequence, or a portion thereof, is inserted, exogenous translational control signals including the ATG initiation codon should be provided. Furthermore, the initiation codon should be in the correct reading frame to ensure translation of the entire insert. Exogenous translational elements and initiation codons may be of various origins, both natural and synthetic. The efficiency of expression may be enhanced by the inclusion of enhancers which are appropriate for the particular cell system which is used, such as those described in the literature (Scharf, et al., Results Probl. Cell Differ. 20: 125-162 (1994)).
  • a host cell strain may be chosen for its ability to modulate the expression of the inserted sequences or to process the expressed protein in the desired fashion.
  • modifications of the polypeptide include, but are not limited to, post-translational modifications such as acetylation, carboxylation, glycosylation, phosphorylation, lipidation, and acylation.
  • Post-translational processing which cleaves a “prepro” form of the protein may also be used to facilitate correct insertion, folding and/or function.
  • Different host cells such as yeast, CHO, He La, MDCK, HEK293, and W138, in addition to bacterial cells, which have or even lack specific cellular machinery and characteristic mechanisms for such post-translational activities, may be chosen to ensure the correct modification and processing of the foreign protein.
  • cell lines which stably express a polynucleotide of interest may be transformed using expression vectors which may contain viral origins of replication and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector. Following the introduction of the vector, cells may be allowed to grow for about 1-2 days in an enriched media before they are switched to selective media. The purpose of the selectable marker is to confer resistance to selection, and its presence allows growth and recovery of cells which successfully express the introduced sequences. Resistant clones of stably transformed cells may be proliferated using tissue culture techniques appropriate to the cell type. Transient production, such as by transient transfection or infection, can also be employed. Exemplary mammalian expression systems that are suitable for transient production include HEK293 and CHO-based systems.
  • selection systems may be used to recover transformed or transduced cell lines. These include, but are not limited to, the herpes simplex virus thymidine kinase (Wigler et al., Cell 11:223-232 (1977)) and adenine phosphoribosyltransferase (Lowy et al., Cell 22:817-823 (1990)) genes which can be employed in tk- or aprt- cells, respectively. Also, antimetabolite, antibiotic or herbicide resistance can be used as the basis for selection; for example, dhfr which confers resistance to methotrexate (Wigler et al., PNAS USA.
  • npt which confers resistance to the aminoglycosides, neomycin and G-418 (Colbere-Garapin et al., J. Mol. Biol. 150: 1-14 (1981)); and als or pat, which confer resistance to chlorsulfuron and phosphinotricin acetyltransferase, respectively (Murry, supra). Additional selectable genes have been described, for example, trpB, which allows cells to utilize indole in place of tryptophan, or hisD, which allows cells to utilize histinol in place of histidine (Hartman & Mulligan, Proc. Natl. Acad. Sci. U.S.A.
  • GFP green fluorescent protein
  • RFP red fluorescent protein
  • YFP fluorescent protein
  • anthocyanins p-glucuronidase and its substrate GUS
  • luciferase and its substrate luciferin being widely used not only to identify transformants, but also to quantify the amount of transient or stable protein expression attributable to a specific vector system (see, e.g., Rhodes et al., Methods Mol. Biol. 55: 121-131 (1995)).
  • high-throughput protein production systems or micro-production systems. Certain aspects may utilize, for example, hexa-histidine fusion tags for protein expression and purification on metal chelate-modified slide surfaces or MagneHis Ni-Particles (see, e.g., Kwon et al., BMC Biotechnol. 9:72, 2009; and Uin et al., Methods Mol Biol. 498: 129-41, 2009)). Also included are high-throughput cell-free protein expression systems (see, e.g., Sitaraman et al., Methods Mol Biol. 498:229-44, 2009). These and related embodiments can be used, for example, to generate microarrays of anti-NRP2 antibodies which can then be used for screening libraries to identify antibodies and antigen-binding domains that interact with the NRP2 polypeptide(s) of interest.
  • Means for producing labeled hybridization or PCR probes for detecting sequences related to polynucleotides include oligolabeling, nick translation, end-labeling or PCR amplification using a labeled nucleotide.
  • the sequences, or any portions thereof may be cloned into a vector for the production of an mRNA probe.
  • Such vectors are known in the art, are commercially available, and may be used to synthesize RNA probes in vitro by addition of an appropriate RNA polymerase such as T7, T3, or SP6 and labeled nucleotides.
  • reporter molecules or labels include radionuclides, enzymes, fluorescent, chemiluminescent, or chromogenic agents as well as substrates, cofactors, inhibitors, magnetic particles, and the like.
  • Host cells transformed with a polynucleotide sequence of interest may be cultured under conditions suitable for the expression and recovery of the protein from cell culture.
  • Certain specific embodiments utilize serum free cell expression systems. Examples include HEK293 cells and CHO cells that can be grown in serum-free medium (see, e.g., Rosser et al., Protein Expr. Purif. 40:237-43, 2005; and U.S. Patent number 6,210,922).
  • An antibody, or antigen-binding fragment thereof, produced by a recombinant cell may be secreted or contained intracellularly depending on the sequence and/or the vector used.
  • expression vectors containing polynucleotides may be designed to contain signal sequences which direct secretion of the encoded polypeptide through a prokaryotic or eukaryotic cell membrane.
  • Other recombinant constructions may be used to join sequences encoding a polypeptide of interest to nucleotide sequence encoding a polypeptide domain which will facilitate purification and/or detection of soluble proteins.
  • cleavable and non-cleavable affinity purification and epitope tags such as avidin, FLAG tags, polyhistidine tags (e.g., 6xHis), cMyc tags, V5-tags, glutathione S-transferase (GST) tags, and others.
  • the protein produced by a recombinant cell can be purified and characterized according to a variety of techniques known in the art.
  • Exemplary systems for performing protein purification and analyzing protein purity include fast protein liquid chromatography (FPLC) (e.g., AKTA and Bio-Rad FPLC systems), high-pressure liquid chromatography (HPLC) (e.g., Beckman and Waters HPLC).
  • FPLC fast protein liquid chromatography
  • HPLC high-pressure liquid chromatography
  • Exemplary chemistries for purification include ion exchange chromatography (e.g., Q, S), size exclusion chromatography, salt gradients, affinity purification (e.g., Ni, Co, FLAG, maltose, glutathione, protein A/G), gel filtration, reverse-phase, ceramic HYPERD® ion exchange chromatography, and hydrophobic interaction columns (HIC), among others known in the art. Also included are analytical methods such as SDS-PAGE (e.g., coomassie, silver stain), immunoblot, Bradford, and ELISA, which may be utilized during any step of the production or purification process, typically to measure the purity of the protein composition.
  • affinity purification e.g., Ni, Co, FLAG, maltose, glutathione, protein A/G
  • gel filtration e.g., reverse-phase, ceramic HYPERD® ion exchange chromatography
  • HIC hydrophobic interaction columns
  • analytical methods such as SDS-PAGE (e.
  • concentrated solutions of anti-NRP2 antibodies may comprise proteins at a concentration of about 5 mg/mL; or about 8 mg/mL; or about 10 mg/mL; about 15 mg/mL; or about 20 mg/mL.
  • compositions may be substantially monodisperse, meaning that an at least one anti-NRP2 antibody exists primarily (i.e., at least about 90%, or greater) in one apparent molecular weight form when assessed for example, by size exclusion chromatography, dynamic light scattering, or analytical ultracentrifiigation.
  • compositions have a purity (on a protein basis) of at least about 90%, or in some aspects at least about 95% purity, or in some embodiments, at least 98% purity. Purity may be determined via any routine analytical method as known in the art.
  • compositions have a high molecular weight aggregate content of less than about 10%, compared to the total amount of protein present, or in some embodiments such compositions have a high molecular weight aggregate content of less than about 5%, or in some aspects such compositions have a high molecular weight aggregate content of less than about 3%, or in some embodiments a high molecular weight aggregate content of less than about 1%.
  • High molecular weight aggregate content may be determined via a variety of analytical techniques including for example, by size exclusion chromatography, dynamic light scattering, or analytical ultracentrifugation .
  • concentration approaches contemplated herein include lyophilization, which is typically employed when the solution contains few soluble components other than the protein of interest. Lyophilization is often performed after HPLC run, and can remove most or all volatile components from the mixture. Also included are ultrafiltration techniques, which typically employ one or more selective permeable membranes to concentrate a protein solution. The membrane allows water and small molecules to pass through and retains the protein; the solution can be forced against the membrane by mechanical pump, gas pressure, or centrifugation, among other techniques.
  • the reagents, anti-NRP2 antibodies, or related agents have a purity of at least about 90%, as measured according to routine techniques in the art.
  • an anti-NRP2 antibody composition has a purity of at least about 95%.
  • an anti-NRP2 antibody composition has a purity of at least about 97% or 98% or 99%.
  • anti-NRP2 antibodies can be of lesser purity, and may have a purity of at least about 50%, 60%, 70%, or 80%. Purity can be measured overall or in relation to selected components, such as other proteins, for example, purity on a protein basis.
  • Purified anti-NRP2 antibodies can also be characterized according to their biological characteristics. Binding affinity and binding kinetics can be measured according to a variety of techniques known in the art, such as Biacore® and related technologies that utilize surface plasmon resonance (SPR), an optical phenomenon that enables detection of unlabeled interactants in real time. SPR-based biosensors can be used in determination of active concentration, screening and characterization in terms of both affinity and kinetics.
  • SPR surface plasmon resonance
  • an anti-NRP2 antibody composition comprises less than about 10% wt/wt high molecular weight aggregates, or less than about 5% wt/wt high molecular weight aggregates, or less than about 2% wt/wt high molecular weight aggregates, or less than about or less than about 1% wt/wt high molecular weight aggregates.
  • Protein-based analytical assays and methods which can be used to assess, for example, protein purity, size, solubility, and degree of aggregation, among other characteristics.
  • Protein purity can be assessed a number of ways. For instance, purity can be assessed based on primary structure, higher order structure, size, charge, hydrophobicity, and glycosylation.
  • methods for assessing primary structure include N- and C-terminal sequencing and peptide-mapping (see, e.g., Allen et al., Biologicals. 24:255-275, 1996)).
  • methods for assessing higher order structure include circular dichroism (see, e.g., Kelly et al., Biochim Biophys Acta.
  • Hydrophobicity can be assessed, for example, by reverse-phase HPLC and hydrophobic interaction chromatography HPLC. Glycosylation can affect pharmacokinetics (e.g., clearance), conformation or stability, receptor binding, and protein function, and can be assessed, for example, by mass spectrometry and nuclear magnetic resonance (NMR) spectroscopy.
  • pharmacokinetics e.g., clearance
  • conformation or stability e.g., conformation or stability
  • receptor binding e.g., and protein function
  • NMR nuclear magnetic resonance
  • certain embodiments include the use of SEC-HPLC to assess protein characteristics such as purity, size (e.g., size homogeneity) or degree of aggregation, and/or to purify proteins, among other uses.
  • SEC also including gel-fdtration chromatography (GFC) and gelpermeation chromatography (GPC) refers to a chromatographic method in which molecules in solution are separated in a porous material based on their size, or more specifically their hydrodynamic volume, diffusion coefficient, and/or surface properties. The process is generally used to separate biological molecules, and to determine molecular weights and molecular weight distributions of polymers.
  • a biological or protein sample (such as a protein extract produced according to the protein expression methods provided herein and known in the art) is loaded into a selected size-exclusion column with a defined stationary phase (the porous material), preferably a phase that does not interact with the proteins in the sample.
  • the stationary phase is composed of inert particles packed into a dense three-dimensional matrix within a glass or steel column.
  • the mobile phase can be pure water, an aqueous buffer, an organic solvent, or a mixture thereof.
  • the stationary-phase particles typically have small pores and/or channels which only allow molecules below a certain size to enter.
  • Protein purity for clinical applications is also discussed, for example, by Anicetti et al. (Trends in Biotechnology. 7:342-349, 1989). More recent techniques for analyzing protein purity include, without limitation, the LabChip GXII, an automated platform for rapid analysis of proteins and nucleic acids, which provides high throughput analysis of titer, sizing, and purity analysis of proteins.
  • clinical grade proteins such as protein fragments and antibodies can be obtained by utilizing a combination of chromatographic materials in at least two orthogonal steps, among other methods (see, e.g., Therapeutic Proteins: Methods and Protocols. Vol. 308, Eds., Smales and James, Humana Press Inc., 2005).
  • protein agents e.g., anti-NRP2 antibodies, and antigen-binding fragments
  • protein agents are substantially endotoxin-free, as measured according to techniques known in the art and described herein.
  • Protein solubility assays are also included. Such assays can be utilized, for example, to determine optimal growth and purification conditions for recombinant production, to optimize the choice of buffer(s), and to optimize the choice of anti-NRP2 antibodies or variants thereof. Solubility or aggregation can be evaluated according to a variety of parameters, including temperature, pH, salts, and the presence or absence of other additives. Examples of solubility screening assays include, without limitation, microplate -based methods of measuring protein solubility using turbidity or other measure as an end point, high-throughput assays for analysis of the solubility of purified recombinant proteins (see, e.g., Stenvall et al., Biochim Biophys Acta.
  • Anti-NRP2 antibodies with increased solubility can be identified or selected for according to routine techniques in the art, including simple in vivo assays for protein solubility (see, e.g., Maxwell et al., Protein Sci. 8: 1908-11, 1999). Protein solubility and aggregation can also be measured by dynamic light scattering techniques. Aggregation is a general term that encompasses several types of interactions or characteristics, including soluble/insoluble, covalent/noncovalent, reversible/irreversible, and native/denatured interactions and characteristics.
  • Dynamic light scattering refers to a technique that can be used to determine the size distribution profde of small particles in suspension or polymers such as proteins in solution. This technique, also referred to as photon correlation spectroscopy (PCS) or quasi-elastic light scattering (QELS), uses scattered light to measure the rate of diffusion of the protein particles. Fluctuations of the scattering intensity can be observed due to the Brownian motion of the molecules and particles in solution.
  • PCS photon correlation spectroscopy
  • QELS quasi-elastic light scattering
  • This motion data can be conventionally processed to derive a size distribution for the sample, wherein the size is given by the Stokes radius or hydrodynamic radius of the protein particle.
  • the hydrodynamic size depends on both mass and shape (conformation).
  • Dynamic scattering can detect the presence of very small amounts of aggregated protein ( ⁇ 0.01% by weight), even in samples that contain a large range of masses. It can also be used to compare the stability of different formulations, including, for example, applications that rely on real-time monitoring of changes at elevated temperatures. Accordingly, certain embodiments include the use of dynamic light scattering to analyze the solubility and/or presence of aggregates in a sample that contains an anti-NRP2 antibody of the present disclosure.
  • compositions that comprise the antibodies, or antigen-binding fragments thereof, described herein, optionally in combination with a suitable carrier.
  • a composition or carrier may be liquid, semi-liquid, semi-solid, or solid.
  • Solutions or suspensions may include, for example, a sterile diluent (such as water), saline solution (e.g., phosphate buffered saline (PBS), physiological saline, Ringer’s solution, isotonic sodium chloride), fixed oil, polyethylene glycol, glycerin, propylene glycol or other synthetic solvent; antimicrobial agents (such as benzyl alcohol and methyl parabens); antioxidants (such as ascorbic acid and sodium bisulfite), chelating agents (such as ethylenediaminetetraacetic acid (EDTA)); and/or buffers (such as acetates, citrates, phosphates, and other organic acids), including combinations of the foregoing.
  • a sterile diluent such as water
  • saline solution e.g., phosphate buffered saline (PBS), physiological saline, Ringer’s solution, isotonic sodium chloride
  • fixed oil poly
  • Suitable carriers are solutions containing thickening and solubilizing agents, such as glucose, polyethylene glycol, polypropylene glycol and mixtures thereof.
  • a surfactant may be added to facilitate the formation of a homogeneous solution or suspension.
  • Surfactants are compounds that non-covalently interact with the antibody, or antigen-binding fragment thereof, so as to facilitate dissolution or homogeneous suspension of the conjugate in the aqueous system.
  • carriers include low molecular weight (e.g., less than about 10 residues) polypeptides or peptides; proteins such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, arginine, or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; sugar alcohols such as mannitol or sorbitol; salt-forming counterions such as sodium; and/or nonionic surfactants such as polysorbate 20 (TWEENTM) polyethylene glycol (PEG), and poloxamers (PLURONICSTM), and the like.
  • TWEENTM polyethylene glycol
  • PLURONICSTM poloxamers
  • the antibody, or antigen-binding fragment thereof is entrapped in microcapsules prepared, for example, by coacervation techniques or by interfacial polymerization (for example, hydroxymethylcellulose or gelatin-microcapsules and poly- (methylmethacylate)microcapsules, respectively), in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nano-particles and nanocapsules), or in macroemulsions.
  • colloidal drug delivery systems for example, liposomes, albumin microspheres, microemulsions, nano-particles and nanocapsules
  • macroemulsions for example, liposomes, albumin microspheres, microemulsions, nano-particles and nanocapsules
  • the particle(s) or liposomes may further comprise other diagnostic agents, such as detectable entities.
  • the antibody, or antigen-binding fragment thereof is a freeze- dried or lyophilized, cryodesiccated.
  • freeze- dried or lyophilized, cryodesiccated refer to a dehydration process of freezing the antibody composition and then reducing the surrounding pressure to allow the frozen water in the composition to sublimate directly from the solid phase to the gas phase.
  • solid compositions such as powders, granules, compressed tablets, pills, capsules, and the like.
  • solid composition contain one or more inert diluents or edible carriers.
  • binders such as carboxymethylcellulose, ethyl cellulose, microcrystalline cellulose, gum tragacanth or gelatin
  • excipients such as starch, lactose or dextrins, disintegrating agents such as alginic acid, sodium alginate, Primogel, com starch and the like.
  • kits comprising one or more of the anti-NRP2 antibodies, or antigen-binding fragments thereof, as described herein, optionally in one or more containers.
  • the kits can include written instructions on how to use and/or prepare the antibodies for use, for example, as detection and/or diagnostic agents.
  • the written instructions describe how to use the antibodies, or antigen-binding fragments thereof, to identify a subject for arginine deprivation therapy, e.g., with arginine depletion agent(s).
  • the kit comprises material(s) for an IHC (e.g., chromogenic IHC) assay or an IF assay.
  • the kit comprises material(s) for an enzyme-linked immunosorbent assay (ELISA) or similar assay, for example, where the antibody, or antigen-binding fragment thereof, is attached or attachable to a solid substrate for performing an ELISA or similar assay.
  • ELISA enzyme-linked immunosorbent assay
  • kits herein may also include a one or more additional therapeutic agents or other components suitable or desired for the indication being treated, or for the desired diagnostic application.
  • An additional therapeutic agent may be contained in a second container, if desired.
  • additional therapeutic agents include NRP2-targeted therapeutic agents, for example, a therapeutic antibody, or antigen-binding fragment thereof, which binds to human NRP2 (see, for example, WO 2019/195770; and WO 2021/067761).
  • Anti-NRP2 antibodies suitable for immunohistochemistry and related uses were generated by immunizing mice via an IP administration with 1 x 10 6 Expi293 cells stably over expressing human NRP2A variant 2 (Origene Technologies Cat#RC220706), (prepared as more fully described below) using standard methodologies. Titers were boosted via S.C. administration of 10 pg/mouse of the corresponding recombinant NRP2 polypeptides listed in Table Nl, using either IFA or Magic Mouse as the adjuvant. Mice were boosted every 2-3 weeks and then screened for initial titer and specificity using the NRP2 polypeptides listed in Table Nl.
  • spleens were isolated from immunized animals and fusion with mouse myeloma cells was performed to generate hybridomas using standard techniques. Fusion, plating into 96-well plates, ELISA screening of hybridomas, expansion and characterization of positive hybridomas (titer and isotype) and freezing of up to 15 hybridomas per antigen, was performed at The Scripps Research Institute (TSRI) Center for Antibody Development and Production. Antibody variable domain sequences were obtained using standard sequencing approaches performed at Lake Pharma, and are provided in Table SI and Table S2.
  • Recombinant antibodies were produced from hybridoma cells after expansion and purified from conditioned medium starting at 2 weeks of culture by flowing over a Protein A affinity column, eluting and storing in Phosphate Buffered Saline (IX PBS), pH 7.4. Each lot was tested for protein concentration, purity and endotoxin level. Purity by SDS-PAGE was routinely >90%.
  • Antibody aNRP2-36v2 was tested for its specificity for binding to NRP2a via ELISA using three different purification lots.
  • Amino acids 23-855 of NRP2v2 (SEQ ID NO: 14) were cloned with the native signal peptide and a C-terminal Myc & 6xHis tag, produced in Expi293 cells, and purified by nickel affinity.
  • a clear flat-bottom Immuno 96W plate (ThermoFisher, #14-245-153) was coated with the NRP2v2 protein at 2ug/mL diluted in IX PBS pH 7.4 (ThermoFisher, #10010031). Plate was coated overnight at 4°C without shaking.
  • the plate was incubated for 1 hour at room temperature with shaking (400rpm). The plate was washed 3 times with 300uL/well of PBST and the HRP conjugated goat anti-mouse IgG secondary antibody (Jackson Immuno, #115-035-071) was applied at a 1:5000 dilution in Casein at 50uL/well. Plate was incubated for 1 hour at room temperature with shaking (400rpm). The plate was washed 3 times with 300uL/well of PBST and the plate was developed with Ultra TMB ELISA substrate (ThermoFisher, #PI34029) at 50uL/well for 7min. The colorimetric reaction was stopped using 50uL/well of Stop Solution (Biolegend, #423001). The signals were read on a BioTek plate reader at 450nm (BioTek PowerWave HT).
  • Antibody aNRP2-36v2 was tested for its binding to different NRP2 domains and to evaluate its cross-reactivity to mouse, rat, and cyno NRP2, as well as testing for potential cross reactivity to human NRP1.
  • Clear flat-bottom Immuno 96W plates (ThermoFisher, #14-245-153) were coated with various NRP2 proteins at 2ug/mL diluted in IX PBS pH 7.4 (ThermoFisher, #10010031).
  • Three different batches of antibody aNRP2-36v2 were tested with proteins (SEQ ID NOs: 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, and 27; see Table Nl). Plates were coated overnight at 4°C without shaking.
  • the plate was washed 3 times with 300uL/well of PBST and the HRP conjugated goat anti-mouse IgG secondary antibody (Jackson Immuno, #115-035- 071) was applied at a 1:5000 dilution in Casein at 50uL/well. Plate was incubated for 1 hour at room temperature with shaking (400rpm). The plate was washed 3 times with 300uL/well of PBST and was developed with Ultra TMB ELISA substrate (ThermoFisher, #PI34029) at 50uL/well for 7min. The colorimetric reaction was stopped using 50uL/well of Stop Solution (Biolegend, #423001). The signals were read on a BioTek plate reader at 450nm (BioTek PowerWave HT).
  • Biolayer interferometry (BLI) experiments were carried out on an Octet RED96e instrument (Sartorius).
  • Antibody aNRP2-36v2 was tested for affinity towards human and cynomolgus NRP2.
  • Antibodies and proteins were diluted in IxPBS, 0.1% BSA, 0.02% Tween 20, pH 7.4.
  • Octet Streptavidin biosensors (Sartorius, 18-5020) were immobilized with biotin-conjugated CaptureSelect anti-LC Kappa (murine) antibodies (Thermo Scientific, 7103152500).
  • the biosensors were dipped into 1 pg/mL aNRP2-36v2 to capture the antibody on the biosensors.
  • the epitope specificity of antibody aNRP2-36v2 binding to NRP2 was tested by incubation with a blocking peptide corresponding to residues 642-659 of NRP2 (SEQ ID NO: 25). This region was determined to be the likely epitope of aNRP2-36v2 based on its lack of binding to cynomolgus monkey NRP2 and an analysis of the sequence differences between human and cynomolgus NRP2 within region ofNRP2 identified above.
  • the region surrounding residue 651 ofNRP2 was considered to be the most likely epitope location because of both the existence of amino acid differences in this region, and the existence of nearby flanking Cys residues which could account for the observed sensitivity of antibody binding to the redox state of NRP2 measured under either reducing or oxidized conditions as shown below.
  • aNRP2-36v2 was captured on BLI biosensors and dipped into NRP2 incubated with increasing amounts of peptide.
  • Antibodies and proteins were diluted in IxPBS, 0. 1% BSA, 0.02% Tween 20, pH 7.4.
  • Octet Streptavidin biosensors (Sartorius, 18-5020) were immobilized with biotin-conjugated CaptureSelect anti-LC Kappa (murine) antibodies (Thermo Scientific, 7103152500). The biosensors were dipped into 1 pg/mL aNRP2-36v2 to capture the antibody on the biosensors.
  • NRP2v2 (23-855) (SEQ ID NO: 14), NRP2v5 (23-832) (SEQ ID NO: 27), mouse NRP2v2 (23-855) (SEQ ID NO: 21), rat NRP2x2 (23-854) (SEQ ID NO: 22), and NRPlv2 (22-602) (SEQ ID NO: 24).
  • the membrane was blocked for 1 hour using a 5% milk 0.05% TBST solution, followed by 1.0 ug/mL of the three lots of aNRP2-36v2 antibody diluted in 5% milk 0.05% TBST.
  • Antibody was incubated on the blots overnight at 4°C with rocking. After overnight incubation 3 washes with 0.05% TBST for 5 minutes each were performed and goat-a-mouse HRP secondary (Jackson Immuno Research, 115-035-071) diluted at 1:5,000 in the 5% milk mixture was applied to the blots for 1 hour. This was followed by 3 more washes with 0.05% TBST for 5 minutes each.
  • the membrane was incubated in SuperSignal West Femto Chemiluminescent (ThermoFisher, PI34096) for 30 seconds and imaged in a Syngene G:Box Chemi XX6.
  • the results demonstrate that antibody aNRP2-36v2 only reacts to the nonreduced proteins NRP2v2 (23-855) (SEQ ID NO: 14) and NRP2v5 (23-832) (SEQ ID NO: 27), or the NRP2a and NRP2b isoform proteins. This data is consistent with the ELISA epitope mapping data.
  • NRP2v2 (23-855) (SEQ ID NO: 14) and NRP2v5 (23-832) (SEQ ID NO: 27) proteins and do not show binding to mouse or rat NRP2, and also do not cross-react with NRPl.
  • NRP2v2 (23-855) (SEQ ID NO: 14) recombinant protein and 20 pg of total protein from cell lysates of Expi293 cells transiently expressing NRP2a isoform 2 (SEQ ID NO: 10) were denatured for 10 minutes at 70°C with IxLDS (ThermoFisher, NP0007) and separated on a 4-12% Bis-Tris Protein Gel (ThermoFisher, NP0335) in IxMOPS buffer (ThermoFisher, NP000102).
  • the gel was then transferred to a nitrocellulose membrane (Fisher, cat.# IB23001) using an iBlot2 (Fisher, cat.# IB21001) for 7min at 20V.
  • the membrane was blocked for 1 hour using a 5% milk 0.05% TBST solution, followed by 1 ug/mL of aNRP2-36v2 antibody with or without 5 pg/mL blocking peptide, diluted in 5% milk 0.05% TBST.
  • a peptide corresponding to NRP2v2 (809-820) (SEQ ID NO: 26) was also used as a control.
  • Antibody was incubated on the blots overnight at 4°C with rocking.
  • FFPE formalin fixed paraffin embedded
  • NBIC control antibody and aNRP2- 36v2 Primary antibodies (NBIC control antibody and aNRP2- 36v2) were diluted in blocking buffer to 20 pg/ml and incubated on the tissue overnight at room temperature in a humidified chamber. For peptide blocking, aNRP2-36v2 was incubated for one hour with 100 pg/ml blocking peptide (SEQ ID NO: 25) prior to addition to the tissue.
  • the images shown in Figure 7 indicate that aNRP2-36v2 detects NRP2 protein expression in the skin of sarcoidosis patients and that NRP2 expression is concentrated within granulomas.
  • Incubation of aNRP2-36v2 with blocking peptide prior to tissue staining prevented detection of NRP2 in sarcoidosis tissue, indicating that aNRP2-36v2 can specifically detect NRP2 in human FFPE tissue sections.

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Abstract

L'invention concerne des anticorps, ainsi que des fragments de liaison à l'antigène de ceux-ci, qui se lient spécifiquement à certains isoformes de neuropiline 2 (NRP2) humaine, avec une faible réactivité croisée à la neuropiline-1 (NRP1) humaine et à la NRP2 non humaine, et qui sont optimisés pour des utilisations diagnostiques telles que des dosages immunohistochimiques ou d'immunofluorescence. L'invention concerne également des compositions et des méthodes associées pour détecter et mesurer la NRP2 humaine dans un échantillon biologique.
PCT/US2023/068511 2022-06-17 2023-06-15 Compositions et méthodes comprenant des anticorps anti-nrp2 WO2023245117A2 (fr)

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